tmp.vcf

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##pipeline_version=DVDS_v1.4.7.4
##resource_version=v1.0.13
##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -11.8399 <= x < -0.3411">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -24069.3954">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -24069.3954 <= x < -11.8399">
##FORMAT=<ID=AD,Number=.,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=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine=<ID=ApplyRecalibration,Version=2014.2-3.1.7-7-gb0ce0a5,Date="Fri Jun 19 21:08:58 PDT 2015",Epoch=1434773338278,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=NO_ET gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/nfs/env/prod/content/genomes/reference/hs37d5/raw/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 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 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 num_threads=1 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 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/hpc/ops/data/Data/ana/WES/2015-06-17.11-55-04.Stanford_Atheletes_24ACE.ACE2_Exome/per_submitted_sample/01_16_DVDS_v1.4.7.4_ACE/01_16.gatk.raw.vcf)] recal_file=(RodBinding name=recal_file source=/hpc/ops/data/Data/ana/WES/2015-06-17.11-55-04.Stanford_Atheletes_24ACE.ACE2_Exome/per_submitted_sample/01_16_DVDS_v1.4.7.4_ACE/01_16.gatk.VQSR.tmp.snp.recal) tranches_file=/hpc/ops/data/Data/ana/WES/2015-06-17.11-55-04.Stanford_Atheletes_24ACE.ACE2_Exome/per_submitted_sample/01_16_DVDS_v1.4.7.4_ACE/01_16.gatk.VQSR.tmp.snp.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine=<ID=CombineVariants,Version=2014.2-3.1.7-7-gb0ce0a5,Date="Fri Jun 19 21:11:33 PDT 2015",Epoch=1434773493551,CommandLineOptions="analysis_type=CombineVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=NO_ET gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/nfs/env/prod/content/genomes/reference/hs37d5/raw/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 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 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 num_threads=1 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 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/hpc/ops/data/Data/ana/WES/2015-06-17.11-55-04.Stanford_Atheletes_24ACE.ACE2_Exome/per_submitted_sample/01_16_DVDS_v1.4.7.4_ACE/01_16.gatk.VQSR.indel.hardfilter.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/hpc/ops/data/Data/ana/WES/2015-06-17.11-55-04.Stanford_Atheletes_24ACE.ACE2_Exome/per_submitted_sample/01_16_DVDS_v1.4.7.4_ACE/01_16.gatk.VQSR.snp.hardfilter.vcf)])] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED 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">
##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=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=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##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=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##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=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio 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">
##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>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##reference=hs37d5.fa
##source=SelectVariants
##INFO=<ID=PMR,Number=1,Type=Character,Description="Major allele from Personalis Major allele Reference">
##ApplyRecalibration="analysis_type input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=hs37d5.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 logging_level=INFO log_to_file=null help=false input=[(RodBinding name=input source=3_01.gatk.raw.vcf)] recal_file=(RodBinding name=recal_file source=3_01.gatk.VQSR.tmp.snp.recal) tranches_file=3_01.gatk.VQSR.tmp.snp.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 ignore_filter=null mode=SNP filter_mismatching_base_and_quals=false"
##CombineVariants="analysis_type input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=hs37d5.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=variant source=3_01.gatk.VQSR.indel.hardfilter.vcf), (RodBinding name=variant2 source=3_01.gatk.VQSR.snp.hardfilter.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false"
##SelectVariants="analysis_type input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=hs37d5.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=3_01.chromosome_1.recal.tmp.all.gatk.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=true excludeFiltered=false regenotype=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_mismatching_base_and_quals=false"
##UnifiedGenotyper="analysis_type input_file=[3_01.chromosome_1.recal.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[1.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=hs37d5.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=CALCULATE_AS_NECESSARY baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=50.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 p_nonref_model=EXACT_INDEPENDENT contamination_fraction_to_filter=0.05 logRemovedReadsFromContaminationFiltering=null exactcallslog=null dbsnp=(RodBinding name=dbsnp source=dbsnp_137.b37.reformatted.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##VariantFiltration="analysis_type input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=hs37d5.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=3_01.gatk.VQSR.indel.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0] filterName=[INDEL_SPECIFIC_FILTERS] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_mismatching_base_and_quals=false"
##bcftools_mergeVersion=1.3-25-g9f5ee21-dirty+htslib-1.3-29-g091c89c
##bcftools_mergeCommand=merge -l vcf_links.txt -O z -m none
##bcftools_normVersion=1.3-25-g9f5ee21-dirty+htslib-1.3-29-g091c89c
##bcftools_normCommand=norm -O z -f /share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -m - tmp.vcf.gz
##bcftools_concatVersion=1.3+htslib-1.3
##bcftools_concatCommand=concat -O z -D -a elite_n269.vcf.gz
##bcftools_normVersion=1.3+htslib-1.3
##bcftools_normCommand=norm -O z -d both elite_n269.vcf.gz
##bcftools_viewVersion=1.3+htslib-1.3
##bcftools_viewCommand=view -r 1:876499 -O z tmp.vcf.gz
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	01_16	01_33	01_34	01_37	01_38	01_41	01_43	01_44	01_50	01_51	01_53	01_59	01_60	01_61	01_62	02_14	02_15	02_17	02_19	02_21	02_23	02_27	02_34	02_35	02_36	02_39	03_38	03_54	03_64	03_65	03_75	03_76	03_77	04_240	04_266	04_267	04_296	07_06__KN049_	07_07__KN075_	07_13__KN500_	07_14__KN501_	07_16	07_17__KN504_	07_32__sp-23_	07_36__sp-45_	07_37__sp-46_	07_38__sp-77_	07_39__sp-79_	07_42__sp-84_	1_02	1_03	1_05	1_06	1_07	1_08	1_09	1_10	1_11	1_12	1_14	1_15	1_17	1_18	1_19	1_25	1_26	1_27	1_28	1_29	1_30	1_32	2_01	2_02	2_03	2_04	2_06	2_29	2_30	3_01	3_02	3_03	3_04	3_05	3_06	3_07	3_08	3_09	3_11	3_12	3_13	3_14	3_15	3_16	3_17	3_18	3_19	3_20	3_21	3_22	3_23	3_24	3_25	3_26	3_27	3_28	3_29	3_30_102A	3_31	3_32	3_33	3_35	3_36	3_37	3_39	3_41	3_42	3_43	3_44	3_45	3_47	3_49	3_51	3_55	3_56	3_57	3_58	3_60	3_61	3_63	3_66_101a	3_67_105a	3_68_10_03	3_71	3_72	3_73	4_04	4_06	4_09	4_106	4_107	4_109	4_110	4_112	4_119	4_122	4_123	4_124	4_125	4_126	4_127	4_13	4_145	4_147	4_14	4_150	4_153	4_157	4_164	4_165	4_16	4_171	4_172	4_174	4_178	4_185	4_18	4_192	4_194	4_200	4_204	4_207	4_209	4_20	4_216	4_217	4_21	4_220	4_229	4_231	4_232	4_233	4_241	4_245	4_24	4_26	4_27	4_281	4_286	4_29	4_300	4_313	4_314	4_318	4_320	4_325	4_32	4_330	4_340	4_345	4_354	4_42	4_44	4_47	4_48	4_59	4_65	4_68	4_73	4_74	4_76	4_77	4_78	4_79	4_81	4_82	4_83	4_91	4_92	4_95	4_97	4_99	6_05	7_18	7_20	7_21	7_23	7_24	7_25	7_26	7_27	7_33	7_40	7_47	7_48	7_49	7_50	7_51	7_52	7_54	s01_63	s01_64	s01_67	s01_68	s01_71	s01_72	s01_73	s01_75	s01_76	s03_78	s03_92	s03_93	s05_04_Sp_M4	s05_05_Sp_M5	s05_06_Sp_M6	s05_07_Sp_M7	s05_08_Sp_M8	s05_09	s05_101_Sp_W1	s05_102_Sp_W2	s05_103_Sp_W3	s05_104_Sp_W4	s05_105_Sp_W5	s05_10	s05_64_XXX	s09_02	s09_03	s09_07	s09_08
1	876499	rs4372192	A	G	456.77	LowQual	DB;Dels=0;FS=0;HaplotypeScore=0;MQ=60;MQ0=0;QD=16.66;VQSLOD=12.82;culprit=QD;set=variant2;PMR=G;BaseQRankSum=0.727;MQRankSum=0.727;ReadPosRankSum=-0.727;DP=1399;AF=0.5;MLEAC=1;MLEAF=0.5;AN=470;AC=450	GT:AD:DP:GQ:PL	1/1:0,5:5:9:111,9,0	1/1:0,3:3:6:82,6,0	1/1:0,6:6:12:167,12,0	1/1:0,4:4:6:84,6,0	1/1:0,3:3:9:117,9,0	1/1:0,1:1:3:40,3,0	1/1:0,4:4:9:115,9,0	1/1:0,1:1:3:39,3,0	1/1:0,4:4:9:117,9,0	1/1:0,1:1:3:40,3,0	1/1:0,13:13:21:289,21,0	1/1:0,2:2:3:45,3,0	1/1:0,4:4:9:118,9,0	1/1:0,9:9:18:246,18,0	1/1:0,6:6:15:192,15,0	1/1:0,3:3:9:116,9,0	1/1:0,4:4:12:145,12,0	./.:.:.:.:.	1/1:0,4:4:9:116,9,0	0/1:1,3:4:29:64,0,29	./.:.:.:.:.	1/1:0,2:2:3:38,3,0	./.:.:.:.:.	0/1:3,5:8:65:145,0,65	0/1:1,3:4:26:76,0,26	./.:.:.:.:.	1/1:0,3:3:6:84,6,0	./.:.:.:.:.	1/1:0,3:3:6:79,6,0	1/1:0,7:7:12:174,12,0	1/1:0,3:3:3:39,3,0	1/1:0,1:1:3:39,3,0	1/1:0,4:4:9:119,9,0	1/1:0,4:4:9:122,9,0	1/1:0,8:8:18:244,18,0	./.:.:.:.:.	1/1:0,4:4:9:105,9,0	0/1:1,2:3:26:39,0,26	0/1:1,6:7:27:115,0,27	1/1:0,1:1:3:37,3,0	1/1:0,4:4:9:121,9,0	1/1:0,5:5:9:128,9,0	1/1:0,1:1:3:38,3,0	1/1:0,7:7:12:163,12,0	./.:.:.:.:.	1/1:0,5:5:12:161,12,0	1/1:0,3:3:9:116,9,0	./.:.:.:.:.	1/1:0,1:1:3:39,3,0	./.:.:.:.:.	1/1:0,2:2:3:45,3,0	1/1:0,4:4:9:119,9,0	1/1:0,6:6:12:164,12,0	0/1:2,3:5:36:73,0,36	0/1:2,5:7:33:115,0,33	1/1:0,3:3:6:83,6,0	1/1:0,3:3:3:38,3,0	1/1:0,2:2:3:45,3,0	1/1:0,3:3:9:112,9,0	1/1:0,2:2:3:45,3,0	./.:.:.:.:.	1/1:0,3:3:6:83,6,0	1/1:0,6:6:6:83,6,0	./.:.:.:.:.	1/1:0,5:5:12:158,12,0	./.:.:.:.:.	1/1:0,2:2:6:67,6,0	1/1:0,2:2:6:77,6,0	./.:.:.:.:.	./.:.:.:.:.	1/1:0,5:5:9:120,9,0	1/1:0,4:4:9:112,9,0	./.:.:.:.:.	1/1:0,7:7:15:198,15,0	1/1:0,9:9:15:196,15,0	1/1:0,8:8:15:192,15,0	1/1:0,3:3:9:113,9,0	./.:.:.:.:.	./.:.:.:.:.	./.:.:.:.:.	1/1:0,6:6:18:232,18,0	1/1:0,6:6:12:158,12,0	1/1:0,6:6:15:188,15,0	1/1:0,4:4:9:116,9,0	1/1:0,11:11:27:346,27,0	1/1:0,8:8:12:154,12,0	1/1:0,6:6:15:180,15,0	1/1:0,10:10:27:334,27,0	1/1:0,9:9:24:318,24,0	1/1:0,5:5:12:153,12,0	./.:.:.:.:.	1/1:0,8:8:18:227,18,0	1/1:0,6:6:12:160,12,0	./.:.:.:.:.	./.:.:.:.:.	1/1:0,4:4:6:82,6,0	0/1:2,2:4:39:39,0,39	1/1:0,5:5:12:163,12,0	1/1:0,6:6:12:160,12,0	1/1:0,4:4:6:83,6,0	1/1:0,4:4:9:120,9,0	1/1:0,7:7:15:196,15,0	1/1:0,3:3:9:116,9,0	1/1:0,10:10:21:273,21,0	1/1:0,4:4:6:78,6,0	1/1:0,11:11:27:333,27,0	1/1:0,9:9:24:300,24,0	1/1:0,1:1:3:38,3,0	1/1:0,7:7:15:202,15,0	1/1:0,2:2:3:39,3,0	1/1:0,10:10:24:310,24,0	./.:.:.:.:.	1/1:0,9:9:24:305,24,0	1/1:0,12:12:30:383,30,0	1/1:0,8:8:15:187,15,0	1/1:0,12:12:33:429,33,0	1/1:0,9:9:24:312,24,0	./.:.:.:.:.	1/1:0,5:5:12:163,12,0	1/1:0,4:4:9:112,9,0	1/1:0,12:12:27:335,27,0	1/1:0,4:4:6:80,6,0	1/1:0,8:8:24:301,24,0	1/1:0,3:3:6:84,6,0	1/1:0,10:10:27:335,27,0	1/1:0,2:2:6:70,6,0	./.:.:.:.:.	1/1:0,4:4:6:82,6,0	1/1:0,6:6:15:199,15,0	1/1:0,5:5:9:123,9,0	1/1:0,3:3:3:45,3,0	1/1:0,2:2:3:45,3,0	1/1:0,2:2:6:73,6,0	1/1:0,4:4:9:118,9,0	1/1:0,6:6:12:146,12,0	1/1:0,8:8:18:234,18,0	1/1:0,2:2:6:76,6,0	1/1:0,6:6:12:150,12,0	1/1:0,6:6:15:204,15,0	1/1:0,15:15:27:367,27,0	1/1:0,7:7:15:201,15,0	1/1:0,11:11:24:315,24,0	1/1:0,10:10:24:315,24,0	1/1:0,1:1:3:40,3,0	1/1:0,14:14:30:395,30,0	1/1:0,6:6:15:202,15,0	1/1:0,13:13:33:415,33,0	0/1:6,5:11:99:134,0,155	1/1:0,15:15:30:401,30,0	1/1:0,9:9:18:251,18,0	1/1:0,3:3:9:112,9,0	1/1:0,9:9:24:306,24,0	1/1:0,9:9:21:257,21,0	1/1:0,6:6:15:195,15,0	1/1:0,6:6:12:165,12,0	1/1:0,9:9:18:238,18,0	1/1:0,17:17:33:429,33,0	1/1:0,18:18:39:484,39,0	1/1:0,12:12:21:252,21,0	1/1:0,8:8:15:196,15,0	1/1:0,10:10:18:242,18,0	0/1:2,5:7:54:133,0,54	1/1:0,8:8:21:273,21,0	1/1:0,4:4:12:152,12,0	1/1:0,17:17:36:485,36,0	1/1:0,6:6:12:154,12,0	0/1:1,10:11:18:214,0,18	1/1:0,5:5:12:161,12,0	1/1:0,10:10:21:259,21,0	1/1:0,9:9:21:263,21,0	1/1:0,10:10:21:269,21,0	1/1:0,3:3:6:79,6,0	1/1:0,5:5:12:148,12,0	1/1:0,4:4:9:107,9,0	1/1:0,11:11:27:351,27,0	1/1:0,5:5:6:84,6,0	1/1:0,8:8:21:261,21,0	0/1:4,5:9:71:141,0,71	1/1:0,8:8:18:231,18,0	0/1:7,10:17:99:259,0,154	1/1:0,5:5:15:195,15,0	1/1:0,1:1:3:39,3,0	1/1:0,16:16:33:439,33,0	1/1:0,3:3:6:83,6,0	1/1:0,4:4:9:123,9,0	1/1:0,3:3:6:72,6,0	1/1:0,3:3:6:70,6,0	1/1:0,15:15:30:390,30,0	1/1:0,4:4:9:110,9,0	1/1:0,5:5:12:154,12,0	1/1:0,3:3:6:81,6,0	1/1:0,3:3:6:81,6,0	1/1:0,5:5:15:183,15,0	1/1:0,5:5:9:122,9,0	./.:.:.:.:.	0/1:4,5:9:60:108,0,60	./.:.:.:.:.	1/1:0,1:1:3:38,3,0	1/1:0,5:5:12:157,12,0	1/1:0,10:10:21:271,21,0	1/1:0,5:5:12:160,12,0	1/1:0,9:9:18:231,18,0	./.:.:.:.:.	1/1:0,3:3:6:84,6,0	1/1:0,2:2:3:38,3,0	0/1:5,6:11:99:203,0,114	./.:.:.:.:.	1/1:0,5:5:12:156,12,0	1/1:0,1:1:3:39,3,0	./.:.:.:.:.	1/1:0,3:3:6:85,6,0	1/1:0,5:5:9:122,9,0	0/1:1,3:4:28:67,0,28	1/1:0,4:4:9:110,9,0	1/1:0,5:5:6:83,6,0	1/1:0,10:10:21:277,21,0	1/1:0,5:5:12:163,12,0	1/1:0,5:5:12:160,12,0	1/1:0,6:6:9:123,9,0	1/1:0,3:3:6:79,6,0	1/1:0,6:6:12:167,12,0	0/1:3,5:8:68:105,0,68	1/1:0,2:2:6:72,6,0	0/1:4,5:9:99:130,0,99	1/1:0,3:3:9:103,9,0	1/1:0,2:2:3:40,3,0	0/1:2,4:6:53:140,0,53	1/1:0,3:3:6:83,6,0	1/1:0,6:6:12:168,12,0	1/1:0,3:3:9:106,9,0	1/1:0,5:5:12:163,12,0	1/1:0,1:1:3:40,3,0	./.:.:.:.:.	1/1:0,3:3:6:83,6,0	1/1:0,4:4:6:79,6,0	1/1:0,11:11:21:283,21,0	./.:.:.:.:.	1/1:0,6:6:9:130,9,0	1/1: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1	876499	.	A	.	50	.	PMR=G;AN=2	GT	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	0/0	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.
1	876499	.	A	.	50	.	PMR=G;AN=2	GT	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	0/0	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.
1	876499	.	A	.	50	.	PMR=G;AN=2	GT	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	0/0	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.