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Question: Switch the position of REF/ALT alleles based on AA (ancestral allele) annotations in VCF
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| ##fileformat=VCFv4.2 | |
| ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> | |
| ##FILTER=<ID=LowQual,Description="Low quality"> | |
| ##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -4.0415 <= x < -0.3987"> | |
| ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -39528.47"> | |
| ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -39528.47 <= x < -4.0415"> | |
| ##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -240139.7406"> | |
| ##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -240139.7406 <= x < -8.9721"> | |
| ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> | |
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> | |
| ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> | |
| ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> | |
| ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | |
| ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> | |
| ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> | |
| ##GATKCommandLine.ApplyRecalibration.2=<ID=ApplyRecalibration,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=15 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT/_LOG/log//PHASE4-VQSR-INDEL-ApplyRECALIB.log help=false version=false input=[(RodBinding name=input source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT//VQSR_PHASE4_snp99.5_raw_indel_2017JUN30.vcf)] recal_file=(RodBinding name=recal_file source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT//Recal_VQSR_INDEL_PHASE4_JOINT.recal) tranches_file=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT/tranches_VQSR_INDEL_PHASE4_JOINT.tranches out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT/VQSR_PHASE4_snp99.5_indel99.0_2017JUN30.vcf ts_filter_level=99.0 useAlleleSpecificAnnotations=false lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Sun Jul 02 19:09:37 HKT 2017",Epoch=1498993777828,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.ApplyRecalibration=<ID=ApplyRecalibration,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=15 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT/_LOG/log//PHASE4-VQSR-SNP-ApplyRECALIB.log help=false version=false input=[(RodBinding name=input source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT//PHASE4_JOINT_snp_indels_ALL_2017JUNE28-new.vcf)] recal_file=(RodBinding name=recal_file source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT//Recal_VQSR_SNP_PHASE4_JOINT.recal) tranches_file=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT/tranches_VQSR_SNP_PHASE4_JOINT.tranches out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT/VQSR_PHASE4_snp99.5_raw_indel_2017JUN30.vcf ts_filter_level=99.5 useAlleleSpecificAnnotations=false lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Sun Jul 02 12:07:34 HKT 2017",Epoch=1498968454049,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.CombineVariants=<ID=CombineVariants,CommandLineOptions="analysis_type=CombineVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL/CONCORD//PHASE4_snp99.5_CHR_HWE_BA_NOCALL_HiCOV-LoCoV-Concord.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL//PHASE4_snp99.5_CHR_HWE_BA_FILTER-HiCoVSAM-NOCALL_10.vcf)])] out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL/COMBINE/PHASE4_snp99.5-CHR_HWE_BA_NOCALL_Combine.vcf genotypemergeoption=UNIQUIFY filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false excludeNonVariants=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Fri Jul 14 15:56:27 HKT 2017",Epoch=1500018987671,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[BadCigar] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=20 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_ALI_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_DINGRI_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ16_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant4 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ23_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant5 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ28_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant6 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ36_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant7 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ37_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant8 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ46_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant9 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ48_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant10 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ50_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant11 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ6_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant12 source=/share_bio/unisvx3/zengchq_group/sohail/_TIBETAN/GATK/VAR_CALL//RAW_QJ7_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant13 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005441-DNA_A09_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant14 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005441-DNA_B09_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant15 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005441-DNA_D12_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant16 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005442-DNA_G01_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant17 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005442-DNA_H01_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant18 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005443-DNA_E09_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant19 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005443-DNA_G01_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant20 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005443-DNA_H01_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant21 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005592-DNA_E05_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant22 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005592-DNA_F05_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant23 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005592-DNA_G05_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant24 source=/share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/VAR_CALL//RAW_LP6005619-DNA_A01_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant25 source=/p200/zengchq_group/sohail/_SHERPA/GATK/VAR_CALL//RAW_SRR1101035_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant26 source=/p200/zengchq_group/sohail/_SHERPA/GATK/VAR_CALL//RAW_SRR1101036_snp_indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant27 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022051.g.vcf)]), (RodBindingCollection [(RodBinding name=variant28 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022052.g.vcf)]), (RodBindingCollection [(RodBinding name=variant29 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022053.g.vcf)]), (RodBindingCollection [(RodBinding name=variant30 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022054.g.vcf)]), (RodBindingCollection [(RodBinding name=variant31 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022055.g.vcf)]), (RodBindingCollection [(RodBinding name=variant32 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022056.g.vcf)]), (RodBindingCollection [(RodBinding name=variant33 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022057.g.vcf)]), (RodBindingCollection [(RodBinding name=variant34 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022058.g.vcf)]), (RodBindingCollection [(RodBinding name=variant35 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022059.g.vcf)]), (RodBindingCollection [(RodBinding name=variant36 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022060.g.vcf)]), (RodBindingCollection [(RodBinding name=variant37 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022061.g.vcf)]), (RodBindingCollection [(RodBinding name=variant38 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022062.g.vcf)]), (RodBindingCollection [(RodBinding name=variant39 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022063.g.vcf)]), (RodBindingCollection [(RodBinding name=variant40 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022064.g.vcf)]), (RodBindingCollection [(RodBinding name=variant41 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022065.g.vcf)]), (RodBindingCollection [(RodBinding name=variant42 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022066.g.vcf)]), (RodBindingCollection [(RodBinding name=variant43 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022067.g.vcf)]), (RodBindingCollection [(RodBinding name=variant44 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022068.g.vcf)]), (RodBindingCollection [(RodBinding name=variant45 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022069.g.vcf)]), (RodBindingCollection [(RodBinding name=variant46 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022070.g.vcf)]), (RodBindingCollection [(RodBinding name=variant47 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022071.g.vcf)]), (RodBindingCollection [(RodBinding name=variant48 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022072.g.vcf)]), (RodBindingCollection [(RodBinding name=variant49 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022073.g.vcf)]), (RodBindingCollection [(RodBinding name=variant50 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022074.g.vcf)]), (RodBindingCollection [(RodBinding name=variant51 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022075.g.vcf)]), (RodBindingCollection [(RodBinding name=variant52 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022076.g.vcf)]), (RodBindingCollection [(RodBinding name=variant53 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022077.g.vcf)]), (RodBindingCollection [(RodBinding name=variant54 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022078.g.vcf)]), (RodBindingCollection [(RodBinding name=variant55 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022079.g.vcf)]), (RodBindingCollection [(RodBinding name=variant56 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022080.g.vcf)]), (RodBindingCollection [(RodBinding name=variant57 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022107.g.vcf)]), (RodBindingCollection [(RodBinding name=variant58 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022108.g.vcf)]), (RodBindingCollection [(RodBinding name=variant59 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022109.g.vcf)]), (RodBindingCollection [(RodBinding name=variant60 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022110.g.vcf)]), (RodBindingCollection [(RodBinding name=variant61 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022111.g.vcf)]), (RodBindingCollection [(RodBinding name=variant62 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022112.g.vcf)]), (RodBindingCollection [(RodBinding name=variant63 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022113.g.vcf)]), (RodBindingCollection [(RodBinding name=variant64 source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-3/GATK/VAR_CALL//RAW_AAGC022114.g.vcf)]), (RodBindingCollection [(RodBinding name=variant65 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_103RQ.g.vcf)]), (RodBindingCollection [(RodBinding name=variant66 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_109EP.g.vcf)]), (RodBindingCollection [(RodBinding name=variant67 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_16EJ.g.vcf)]), (RodBindingCollection [(RodBinding name=variant68 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_31CE.g.vcf)]), (RodBindingCollection [(RodBinding name=variant69 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_40JI.g.vcf)]), (RodBindingCollection [(RodBinding name=variant70 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_43AM.g.vcf)]), (RodBindingCollection [(RodBinding name=variant71 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_50JB.g.vcf)]), (RodBindingCollection [(RodBinding name=variant72 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_52AA.g.vcf)]), (RodBindingCollection [(RodBinding name=variant73 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_53JR.g.vcf)]), (RodBindingCollection [(RodBinding name=variant74 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_55EC.g.vcf)]), (RodBindingCollection [(RodBinding name=variant75 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_56AM.g.vcf)]), (RodBindingCollection [(RodBinding name=variant76 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_63PF.g.vcf)]), (RodBindingCollection [(RodBinding name=variant77 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_72DA.g.vcf)]), (RodBindingCollection [(RodBinding name=variant78 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_76AS.g.vcf)]), (RodBindingCollection [(RodBinding name=variant79 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_77JN.g.vcf)]), (RodBindingCollection [(RodBinding name=variant80 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_7PCE.g.vcf)]), (RodBindingCollection [(RodBinding name=variant81 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_82JC.g.vcf)]), (RodBindingCollection [(RodBinding name=variant82 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_93BS.g.vcf)]), (RodBindingCollection [(RodBinding name=variant83 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_96JP.g.vcf)]), (RodBindingCollection [(RodBinding name=variant84 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL//RAW_98AC.g.vcf)]), (RodBindingCollection [(RodBinding name=variant85 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_QUECHUA/_GATK/VAR-CALL//RAW_LP6005677-DNA_E01.g.vcf)]), (RodBindingCollection [(RodBinding name=variant86 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_QUECHUA/_GATK/VAR-CALL//RAW_LP6005677-DNA_F01.g.vcf)]), (RodBindingCollection [(RodBinding name=variant87 source=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_QUECHUA/_GATK/VAR-CALL//RAW_LP6005519-DNA_G02.g.vcf)]), (RodBindingCollection [(RodBinding name=variant88 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005441-DNA_B07.g.vcf)]), (RodBindingCollection [(RodBinding name=variant89 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005441-DNA_C05.g.vcf)]), (RodBindingCollection [(RodBinding name=variant90 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005441-DNA_C08.g.vcf)]), (RodBindingCollection [(RodBinding name=variant91 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005441-DNA_D04.g.vcf)]), (RodBindingCollection [(RodBinding name=variant92 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005441-DNA_D05.g.vcf)]), (RodBindingCollection [(RodBinding name=variant93 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005441-DNA_D08.g.vcf)]), (RodBindingCollection [(RodBinding name=variant94 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005441-DNA_F12.g.vcf)]), (RodBindingCollection [(RodBinding name=variant95 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005442-DNA_B01.g.vcf)]), (RodBindingCollection [(RodBinding name=variant96 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005443-DNA_A02.g.vcf)]), (RodBindingCollection [(RodBinding name=variant97 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005443-DNA_B01.g.vcf)]), (RodBindingCollection [(RodBinding name=variant98 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005443-DNA_B02.g.vcf)]), (RodBindingCollection [(RodBinding name=variant99 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005443-DNA_E01.g.vcf)]), (RodBindingCollection [(RodBinding name=variant100 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005443-DNA_F01.g.vcf)]), (RodBindingCollection [(RodBinding name=variant101 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_LP6005592-DNA_D03.g.vcf)]), (RodBindingCollection [(RodBinding name=variant102 source=/share_bio/unisvx3/zengchq_group/sohail/_ETHNIC/_GATK/8_VAR-CALL//RAW_SS6004469.g.vcf)]), (RodBindingCollection [(RodBinding name=variant103 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP31_4.g.vcf)]), (RodBindingCollection [(RodBinding name=variant104 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP31_5.g.vcf)]), (RodBindingCollection [(RodBinding name=variant105 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP32_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant106 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP38_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant107 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP38_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant108 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP42_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant109 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP45_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant110 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP45_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant111 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP47_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant112 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP47_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant113 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP49_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant114 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP49_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant115 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP50_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant116 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP50_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant117 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP55_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant118 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP55_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant119 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP58_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant120 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP58_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant121 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP59_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant122 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP64_2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant123 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP64_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant124 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP67_5.g.vcf)]), (RodBindingCollection [(RodBinding name=variant125 source=/p200/zengchq_group/sohail/_HM-SAMPLES//RAW_HMP72_3.g.vcf)]), (RodBindingCollection [(RodBinding name=variant126 source=/share_bio/unisvx3/zengchq_group/sohail/_HM-SAMPLES/GATK/VAR-CALL//RAW_HMP67_4.g.vcf)])] out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT/PHASE4_JOINT_snp_indels_ALL_2017JUNE28-new.vcf includeNonVariantSites=false uniquifySamples=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_num_PL_values=100 input_prior=[] sample_ploidy=2 annotation=[] group=[StandardAnnotation] dbsnp=(RodBinding name=dbsnp source=/share_bio/unisvx3/zengchq_group/sohail/Ref//dbsnp_138.b37.vcf) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jun 28 12:27:02 CST 2017",Epoch=1498624022719,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/BQSR//50JB_BQSR.bam] showFullBamList=false read_buffer_size=null read_filter=[BadCigar] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=50 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=/share_bio/unisvx3/zengchq_group/sohail/_ANDEANS/_GATK/VAR_CALL/_LOG/log//HC-4.log help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name=dbsnp source=/share_bio/unisvx3/zengchq_group/sohail/Ref//dbsnp_138.b37.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Mar 29 14:14:43 HKT 2017",Epoch=1490768083716,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.SelectVariants.2=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-VAR/_LOG/log//PHASE4-JOINT-SelectSNPs-CHR.log help=false version=false variant=(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-VAR//PHASE4_snp99.5_only_2017JUN30.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-VAR/PHASE4_snp99.5_only_CHR_2017JUN30.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jul 05 11:42:16 HKT 2017",Epoch=1499226136876,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.SelectVariants.3=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-BA/_LOG/log//Phase4-Select-BA.log help=false version=false variant=(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/PLINK/SELECT-SNP//PHASE4_snp99.5_only_CHR_HWE_P20new.recode.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-BA/PHASE4_snp99.5_CHR_HWE_BA_FILTER.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=BIALLELIC keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Sun Jul 09 23:57:54 HKT 2017",Epoch=1499615874196,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.SelectVariants.4=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-BA//PHASE4_snp99.5_CHR_HWE_BA_FILTER.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-BA/SEP-SAMPLE/PHASE4_snp99.5_CHR_HWE_BA_FILTER-LoCoVSamples.vcf sample_name=[] sample_expressions=null sample_file=[/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-BA/SEP-SAMPLE/LoCOV-SAMPLELIST.txt] exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=BIALLELIC keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Mon Jul 10 11:32:01 HKT 2017",Epoch=1499657521554,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.SelectVariants.5=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-BA/SEP-SAMPLE//PHASE4_snp99.5_CHR_HWE_BA_FILTER-LoCoVSamples.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name=concordance source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL//PHASE4_snp99.5_CHR_HWE_BA_FILTER-HiCoVSAM-NOCALL_10.vcf) out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL/CONCORD/PHASE4_snp99.5_CHR_HWE_BA_NOCALL_HiCOV-LoCoV-Concord.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Fri Jul 14 09:51:06 HKT 2017",Epoch=1499997066797,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.SelectVariants.6=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[1] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL/COMBINE//PHASE4_snp99.5-CHR_HWE_BA_NOCALL_Combine_RN1.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/EPO-AA/SELECT-CHR/PHASE4-CHR1.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Jul 20 19:22:19 HKT 2017",Epoch=1500549739085,Version=3.6-0-g89b7209> | |
| ##GATKCommandLine.SelectVariants.7=<ID=SelectVariants,Version=3.6-0-g89b7209,Date="Tue Aug 01 14:48:54 HKT 2017",Epoch=1501570134220,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/EPO-AA/FILL-AA//PHASE4_snp99.5-CHR_HWE_BA_NOCALL_Combine_RN1-AA.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/SELECTION/FREQ/SHP/PHASE4_snp99.5-CHR_FINAL_SHERPA-AA.vcf sample_name=[] sample_expressions=null sample_file=[/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/_POP-SPECIFIC-SNP/SHP/SHP.txt] exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=BIALLELIC keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> | |
| ##GATKCommandLine.SelectVariants=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=5 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-VAR/_LOG/log//PHASE4-JOINT-SelectSNPs.log help=false version=false variant=(RodBinding name=variant source=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/GATK/FINAL-JOINT//VQSR_PHASE4_snp99.5_indel99.0_2017JUN30.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/SELECT-VAR/PHASE4_snp99.5_only_2017JUN30.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jul 05 11:14:17 HKT 2017",Epoch=1499224457660,Version=3.6-0-g89b7209> | |
| ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) | |
| ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) | |
| ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) | |
| ##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) | |
| ##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) | |
| ##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) | |
| ##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) | |
| ##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) | |
| ##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) | |
| ##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) | |
| ##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) | |
| ##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) | |
| ##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) | |
| ##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) | |
| ##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) | |
| ##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) | |
| ##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) | |
| ##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) | |
| ##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) | |
| ##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) | |
| ##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) | |
| ##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) | |
| ##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) | |
| ##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) | |
| ##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) | |
| ##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) | |
| ##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) | |
| ##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) | |
| ##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) | |
| ##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) | |
| ##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) | |
| ##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) | |
| ##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) | |
| ##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) | |
| ##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) | |
| ##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) | |
| ##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) | |
| ##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) | |
| ##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) | |
| ##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) | |
| ##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) | |
| ##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) | |
| ##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) | |
| ##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) | |
| ##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) | |
| ##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) | |
| ##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) | |
| ##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) | |
| ##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) | |
| ##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) | |
| ##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) | |
| ##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) | |
| ##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) | |
| ##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) | |
| ##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) | |
| ##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) | |
| ##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) | |
| ##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) | |
| ##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) | |
| ##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) | |
| ##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) | |
| ##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) | |
| ##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) | |
| ##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) | |
| ##GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive) | |
| ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README"> | |
| ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | |
| ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> | |
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> | |
| ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> | |
| ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> | |
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> | |
| ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> | |
| ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> | |
| ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> | |
| ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> | |
| ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> | |
| ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> | |
| ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> | |
| ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> | |
| ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> | |
| ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> | |
| ##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants"> | |
| ##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants"> | |
| ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> | |
| ##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality"> | |
| ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | |
| ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> | |
| ##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model"> | |
| ##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"> | |
| ##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants"> | |
| ##VcfRenameSamplesCmdLine=-o /share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL/COMBINE//PHASE4_snp99.5-CHR_HWE_BA_NOCALL_Combine_RN1.vcf -f /share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL/COMBINE//renamesample.txt -E /share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/VAR-FILTER/NO-CALL/COMBINE//PHASE4_snp99.5-CHR_HWE_BA_NOCALL_Combine.vcf | |
| ##VcfRenameSamplesHtsJdkHome=lib/com/github/samtools/htsjdk/2.9.1/htsjdk-2.9.1.jar | |
| ##VcfRenameSamplesHtsJdkVersion=2.9.1 | |
| ##VcfRenameSamplesVersion=02fa35350f66938cbbbf14b590aec49b8f67e514 | |
| ##contig=<ID=1,length=249250621> | |
| ##contig=<ID=2,length=243199373> | |
| ##contig=<ID=3,length=198022430> | |
| ##contig=<ID=4,length=191154276> | |
| ##contig=<ID=5,length=180915260> | |
| ##contig=<ID=6,length=171115067> | |
| ##contig=<ID=7,length=159138663> | |
| ##contig=<ID=8,length=146364022> | |
| ##contig=<ID=9,length=141213431> | |
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| ##reference=file:///share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa | |
| ##source=SelectVariants | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AAGC022072 AAGC022073 AAGC022074 AAGC022075 AAGC022076 LP6005592-DNA_E05 LP6005592-DNA_F05 SHERPA-001 SHERPA-002 | |
| 1 10575 . C G 67.27 PASS AA=.;AC=0;AF=0.00;AN=18;DP=85;set=Intersection GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 0/0:11,0:11:30:0,30,450 0/0:7,0:7:21:0,21,226 0/0:9,0:9:24:0,24,360 0/0:6,0:6:18:0,18,168 0/0:26,0:26:60:0,60,900 0/0:7,0:7:21:0,21,218 0/0:10,0:10:27:0,27,405 0/0:8,0:8:24:0,24,246 | |
| 1 12882 . C G 660.23 PASS AA=c;AC=0;AF=0.00;AN=18;DP=143;set=Intersection GT:AD:DP:GQ:PL 0/0:7,0:7:21:0,21,253 0/0:11,0:11:33:0,33,377 0/0:12,0:12:36:0,36,417 0/0:23,0:23:66:0,66,990 0/0:16,0:16:13:0,13,470 0/0:29,0:29:81:0,81,839 0/0:24,0:24:63:0,63,945 0/0:15,0:15:45:0,45,481 0/0:6,0:6:18:0,18,193 | |
| 1 13079 . C G 1594.47 PASS AA=c;AC=3;AF=0.167;AN=18;DP=340;set=Intersection GT:AD:DP:GQ:PL 0/1:10,4:14:78:78,0,226 0/1:32,4:36:9:9,0,744 0/0:29,3:32:4:0,4,710 0/0:37,0:37:99:0,109,1206 0/0:56,4:60:61:0,61,1501 0/0:33,0:33:99:0,99,1155 0/1:51,8:59:41:41,0,1276 0/0:55,0:55:0:0,0,1269 0/0:14,0:14:42:0,42,425 | |
| 1 17730 . C A 9050.45 PASS AA=-;AC=2;AF=0.111;AN=18;DP=230;set=Intersection GT:AD:DP:GQ:PGT:PID:PL 0/0:28,0:28:48:.:.:0,48,696 0/0:31,0:31:93:.:.:0,93,959 0/0:28,2:30:1:0|1:17722_A_G:0,1,1171 0/0:46,0:46:99:.:.:0,113,1434 0/0:35,0:35:69:.:.:0,69,1054 0/0:27,0:27:46:.:.:0,46,884 0/1:9,4:13:99:0|1:17722_A_G:141,0,617 0/1:7,2:9:63:0|1:17722_A_G:63,0,320 0/0:11,0:11:14:.:.:0,14,274 | |
| 1 49272 rs370116346 G A 397.31 PASS AA=N;AC=4;AF=0.286;AN=14;DP=180;set=Intersection GT:AD:DP:GQ:PL 1/1:0,3:3:9:95,9,0 0/0:25,2:27:28:0,28,742 0/0:31,0:31:90:0,90,1350 1/1:0,4:4:12:125,12,0 0/0:36,4:40:1:0,1,939 0/0:36,0:36:81:0,81,1215 ./.:0,0:0:.:0,0,0 0/0:39,0:39:83:0,83,1138 ./.:0,0:0:.:0,0,0 | |
| 1 936210 rs3121569 C A 124552 PASS AA=A;AC=17;AF=0.944;AN=18;DP=224;set=Intersection GT:AD:DP:GQ:PGT:PID:PL 1/1:0,37:37:99:.:.:1098,108,0 1/1:0,23:23:69:1|1:936194_A_G:987,69,0 1/1:0,29:29:85:.:.:860,85,0 1/1:0,28:28:83:.:.:911,83,0 1/1:0,20:20:60:.:.:673,60,0 1/1:0,24:24:75:1|1:936194_A_G:1071,75,0 1/1:0,29:29:87:.:.:1011,87,0 0/1:7,7:14:99:.:.:206,0,144 1/1:1,19:20:34:.:.:514,34,0 |
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| ##fileformat=VCFv4.1 | |
| ##fileDate=06082017_14h14m53s | |
| ##source=SHAPEIT2.v837 | |
| ##log_file=/share_bio/unisvx3/zengchq_group/sohail/_PHASE-4/VAR-PROCESS/_PHASING/DENOVO/VCF/_LOG/log//PHASE4-CHR-1.log | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype"> | |
| ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README"> | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 103-RQ 109-EP 16-EJ 31-CE 40-JI 43-AM 50-JB 52-AA | |
| 1 10575 . C G . PASS AA=. GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 | |
| 1 12882 . C G . PASS AA=c GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 | |
| 1 13079 . C G . PASS AA=c GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 | |
| 1 13110 . G A . PASS AA=g GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 | |
| 1 13116 rs201725126 T G . PASS AA=t GT 1|1 0|0 0|0 0|0 1|1 0|0 0|0 | |
| 1 13118 rs200579949 A G . PASS AA=a GT 1|1 0|0 0|0 0|0 1|1 0|0 0|0 | |
| 1 13143 . G C . PASS AA=g GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 | |
| 1 13178 . G A . PASS AA=g GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 | |
| 1 13273 . G C . PASS AA=g GT 0|0 0|0 1|1 1|1 1|1 0|1 0|1 0|1 |
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