Created
November 29, 2016 23:56
-
-
Save dwaggott/1d36e77a1f87ec3d7c525e3ee7a8ae00 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ##fileformat=VCFv4.2 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> | |
| ##FILTER=<ID=LowQual,Description="Low quality"> | |
| ##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.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.6-0-g89b7209,Date="Fri Aug 26 14:58:54 PDT 2016",Epoch=1472248734319,CommandLineOptions="analysis_type=GenotypeGVCFs 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=/home/lsturm/apps/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.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=8 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=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_02.g.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_03.g.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_05.g.vcf)]), (RodBindingCollection [(RodBinding name=variant4 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_06.g.vcf)]), (RodBindingCollection [(RodBinding name=variant5 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_07.g.vcf)]), (RodBindingCollection [(RodBinding name=variant6 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_08.g.vcf)]), (RodBindingCollection [(RodBinding name=variant7 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_09.g.vcf)]), (RodBindingCollection [(RodBinding name=variant8 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_10.g.vcf)]), (RodBindingCollection [(RodBinding name=variant9 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_11.g.vcf)]), (RodBindingCollection [(RodBinding name=variant10 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_12.g.vcf)]), (RodBindingCollection [(RodBinding name=variant11 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_14.g.vcf)]), (RodBindingCollection [(RodBinding name=variant12 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_15.g.vcf)]), (RodBindingCollection [(RodBinding name=variant13 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_16.g.vcf)]), (RodBindingCollection [(RodBinding name=variant14 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_17.g.vcf)]), (RodBindingCollection [(RodBinding name=variant15 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_18.g.vcf)]), (RodBindingCollection [(RodBinding name=variant16 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_19.g.vcf)]), (RodBindingCollection [(RodBinding name=variant17 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_25.g.vcf)]), (RodBindingCollection [(RodBinding name=variant18 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_26.g.vcf)]), (RodBindingCollection [(RodBinding name=variant19 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_27.g.vcf)]), (RodBindingCollection [(RodBinding name=variant20 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_28.g.vcf)]), (RodBindingCollection [(RodBinding name=variant21 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_29.g.vcf)]), (RodBindingCollection [(RodBinding name=variant22 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_30.g.vcf)]), (RodBindingCollection [(RodBinding name=variant23 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_32.g.vcf)]), (RodBindingCollection [(RodBinding name=variant24 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_33.g.vcf)]), (RodBindingCollection [(RodBinding name=variant25 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_34.g.vcf)]), (RodBindingCollection [(RodBinding name=variant26 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_37.g.vcf)]), (RodBindingCollection [(RodBinding name=variant27 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_38.g.vcf)]), (RodBindingCollection [(RodBinding name=variant28 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_41.g.vcf)]), (RodBindingCollection [(RodBinding name=variant29 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_43.g.vcf)]), (RodBindingCollection [(RodBinding name=variant30 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_44.g.vcf)]), (RodBindingCollection [(RodBinding name=variant31 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_50.g.vcf)]), (RodBindingCollection [(RodBinding name=variant32 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_51.g.vcf)]), (RodBindingCollection [(RodBinding name=variant33 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_53.g.vcf)]), (RodBindingCollection [(RodBinding name=variant34 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_59.g.vcf)]), (RodBindingCollection [(RodBinding name=variant35 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_60.g.vcf)]), (RodBindingCollection [(RodBinding name=variant36 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_61.g.vcf)]), (RodBindingCollection [(RodBinding name=variant37 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_62.g.vcf)]), (RodBindingCollection [(RodBinding name=variant38 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_63.g.vcf)]), (RodBindingCollection [(RodBinding name=variant39 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_64.g.vcf)]), (RodBindingCollection [(RodBinding name=variant40 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_67.g.vcf)]), (RodBindingCollection [(RodBinding name=variant41 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_68.g.vcf)]), (RodBindingCollection [(RodBinding name=variant42 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_71.g.vcf)]), (RodBindingCollection [(RodBinding name=variant43 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_72.g.vcf)]), (RodBindingCollection [(RodBinding name=variant44 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_73.g.vcf)]), (RodBindingCollection [(RodBinding name=variant45 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_75.g.vcf)]), (RodBindingCollection [(RodBinding name=variant46 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/01_76.g.vcf)]), (RodBindingCollection [(RodBinding name=variant47 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_01.g.vcf)]), (RodBindingCollection [(RodBinding name=variant48 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_02.g.vcf)]), (RodBindingCollection [(RodBinding name=variant49 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_03.g.vcf)]), (RodBindingCollection [(RodBinding name=variant50 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_04.g.vcf)]), (RodBindingCollection [(RodBinding name=variant51 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_06.g.vcf)]), (RodBindingCollection [(RodBinding name=variant52 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_14.g.vcf)]), (RodBindingCollection [(RodBinding name=variant53 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_15.g.vcf)]), (RodBindingCollection [(RodBinding name=variant54 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_17.g.vcf)]), (RodBindingCollection [(RodBinding name=variant55 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_19.g.vcf)]), (RodBindingCollection [(RodBinding name=variant56 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_21.g.vcf)]), (RodBindingCollection [(RodBinding name=variant57 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_23.g.vcf)]), (RodBindingCollection [(RodBinding name=variant58 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_27.g.vcf)]), (RodBindingCollection [(RodBinding name=variant59 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_29.g.vcf)]), (RodBindingCollection [(RodBinding name=variant60 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_30.g.vcf)]), (RodBindingCollection [(RodBinding name=variant61 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_34.g.vcf)]), (RodBindingCollection [(RodBinding name=variant62 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_35.g.vcf)]), (RodBindingCollection [(RodBinding name=variant63 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_36.g.vcf)]), (RodBindingCollection [(RodBinding name=variant64 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/02_39.g.vcf)]), (RodBindingCollection [(RodBinding name=variant65 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_01.g.vcf)]), (RodBindingCollection [(RodBinding name=variant66 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_02.g.vcf)]), (RodBindingCollection [(RodBinding name=variant67 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_03.g.vcf)]), (RodBindingCollection [(RodBinding name=variant68 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_04.g.vcf)]), (RodBindingCollection [(RodBinding name=variant69 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_05.g.vcf)]), (RodBindingCollection [(RodBinding name=variant70 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_06.g.vcf)]), (RodBindingCollection [(RodBinding name=variant71 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_07.g.vcf)]), (RodBindingCollection [(RodBinding name=variant72 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_08.g.vcf)]), (RodBindingCollection [(RodBinding name=variant73 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_09.g.vcf)]), (RodBindingCollection [(RodBinding name=variant74 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_11.g.vcf)]), (RodBindingCollection [(RodBinding name=variant75 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_12.g.vcf)]), (RodBindingCollection [(RodBinding name=variant76 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_13.g.vcf)]), (RodBindingCollection [(RodBinding name=variant77 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_14.g.vcf)]), (RodBindingCollection [(RodBinding name=variant78 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_15.g.vcf)]), (RodBindingCollection [(RodBinding name=variant79 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_16.g.vcf)]), (RodBindingCollection [(RodBinding name=variant80 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_17.g.vcf)]), (RodBindingCollection [(RodBinding name=variant81 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_18.g.vcf)]), (RodBindingCollection [(RodBinding name=variant82 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_19.g.vcf)]), (RodBindingCollection [(RodBinding name=variant83 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_20.g.vcf)]), (RodBindingCollection [(RodBinding name=variant84 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_21.g.vcf)]), (RodBindingCollection [(RodBinding name=variant85 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_22.g.vcf)]), (RodBindingCollection [(RodBinding name=variant86 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_23.g.vcf)]), (RodBindingCollection [(RodBinding name=variant87 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_24.g.vcf)]), (RodBindingCollection [(RodBinding name=variant88 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_25.g.vcf)]), (RodBindingCollection [(RodBinding name=variant89 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_26.g.vcf)]), (RodBindingCollection [(RodBinding name=variant90 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_27.g.vcf)]), (RodBindingCollection [(RodBinding name=variant91 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_28.g.vcf)]), (RodBindingCollection [(RodBinding name=variant92 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_29.g.vcf)]), (RodBindingCollection [(RodBinding name=variant93 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_30_102A.g.vcf)]), (RodBindingCollection [(RodBinding name=variant94 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_31.g.vcf)]), (RodBindingCollection [(RodBinding name=variant95 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_32.g.vcf)]), (RodBindingCollection [(RodBinding name=variant96 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_33.g.vcf)]), (RodBindingCollection [(RodBinding name=variant97 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_35.g.vcf)]), (RodBindingCollection [(RodBinding name=variant98 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_36.g.vcf)]), (RodBindingCollection [(RodBinding name=variant99 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_37.g.vcf)]), (RodBindingCollection [(RodBinding name=variant100 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_38.g.vcf)]), (RodBindingCollection [(RodBinding name=variant101 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_39.g.vcf)]), (RodBindingCollection [(RodBinding name=variant102 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_41.g.vcf)]), (RodBindingCollection [(RodBinding name=variant103 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_42.g.vcf)]), (RodBindingCollection [(RodBinding name=variant104 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_43.g.vcf)]), (RodBindingCollection [(RodBinding name=variant105 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_44.g.vcf)]), (RodBindingCollection [(RodBinding name=variant106 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_45.g.vcf)]), (RodBindingCollection [(RodBinding name=variant107 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_47.g.vcf)]), (RodBindingCollection [(RodBinding name=variant108 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_49.g.vcf)]), (RodBindingCollection [(RodBinding name=variant109 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_51.g.vcf)]), (RodBindingCollection [(RodBinding name=variant110 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_54.g.vcf)]), (RodBindingCollection [(RodBinding name=variant111 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_55.g.vcf)]), (RodBindingCollection [(RodBinding name=variant112 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_56.g.vcf)]), (RodBindingCollection [(RodBinding name=variant113 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_57.g.vcf)]), (RodBindingCollection [(RodBinding name=variant114 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_58.g.vcf)]), (RodBindingCollection [(RodBinding name=variant115 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_60.g.vcf)]), (RodBindingCollection [(RodBinding name=variant116 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_61.g.vcf)]), (RodBindingCollection [(RodBinding name=variant117 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_63.g.vcf)]), (RodBindingCollection [(RodBinding name=variant118 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_64.g.vcf)]), (RodBindingCollection [(RodBinding name=variant119 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_65.g.vcf)]), (RodBindingCollection [(RodBinding name=variant120 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_66_101a.g.vcf)]), (RodBindingCollection [(RodBinding name=variant121 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_67_105a.g.vcf)]), (RodBindingCollection [(RodBinding name=variant122 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_68_10_03.g.vcf)]), (RodBindingCollection [(RodBinding name=variant123 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_71.g.vcf)]), (RodBindingCollection [(RodBinding name=variant124 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_72.g.vcf)]), (RodBindingCollection [(RodBinding name=variant125 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_73.g.vcf)]), (RodBindingCollection [(RodBinding name=variant126 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_75.g.vcf)]), (RodBindingCollection [(RodBinding name=variant127 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_76.g.vcf)]), (RodBindingCollection [(RodBinding name=variant128 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_77.g.vcf)]), (RodBindingCollection [(RodBinding name=variant129 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_78.g.vcf)]), (RodBindingCollection [(RodBinding name=variant130 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_92.g.vcf)]), (RodBindingCollection [(RodBinding name=variant131 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/03_93.g.vcf)]), (RodBindingCollection [(RodBinding name=variant132 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_04.g.vcf)]), (RodBindingCollection [(RodBinding name=variant133 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_06.g.vcf)]), (RodBindingCollection [(RodBinding name=variant134 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_09.g.vcf)]), (RodBindingCollection [(RodBinding name=variant135 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_106.g.vcf)]), (RodBindingCollection [(RodBinding name=variant136 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_107.g.vcf)]), (RodBindingCollection [(RodBinding name=variant137 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_109.g.vcf)]), (RodBindingCollection [(RodBinding name=variant138 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_110.g.vcf)]), (RodBindingCollection [(RodBinding name=variant139 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_119.g.vcf)]), (RodBindingCollection [(RodBinding name=variant140 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_122.g.vcf)]), (RodBindingCollection [(RodBinding name=variant141 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_123.g.vcf)]), (RodBindingCollection [(RodBinding name=variant142 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_124.g.vcf)]), (RodBindingCollection [(RodBinding name=variant143 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_125.g.vcf)]), (RodBindingCollection [(RodBinding name=variant144 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_126.g.vcf)]), (RodBindingCollection [(RodBinding name=variant145 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_127.g.vcf)]), (RodBindingCollection [(RodBinding name=variant146 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_13.g.vcf)]), (RodBindingCollection [(RodBinding name=variant147 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_14.g.vcf)]), (RodBindingCollection [(RodBinding name=variant148 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_145.g.vcf)]), (RodBindingCollection [(RodBinding name=variant149 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_147.g.vcf)]), (RodBindingCollection [(RodBinding name=variant150 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_150.g.vcf)]), (RodBindingCollection [(RodBinding name=variant151 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_153.g.vcf)]), (RodBindingCollection [(RodBinding name=variant152 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_157.g.vcf)]), (RodBindingCollection [(RodBinding name=variant153 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_16.g.vcf)]), (RodBindingCollection [(RodBinding name=variant154 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_164.g.vcf)]), (RodBindingCollection [(RodBinding name=variant155 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_165.g.vcf)]), (RodBindingCollection [(RodBinding name=variant156 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_171.g.vcf)]), (RodBindingCollection [(RodBinding name=variant157 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_172.g.vcf)]), (RodBindingCollection [(RodBinding name=variant158 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_174.g.vcf)]), (RodBindingCollection [(RodBinding name=variant159 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_178.g.vcf)]), (RodBindingCollection [(RodBinding name=variant160 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_18.g.vcf)]), (RodBindingCollection [(RodBinding name=variant161 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_185.g.vcf)]), (RodBindingCollection [(RodBinding name=variant162 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_192.g.vcf)]), (RodBindingCollection [(RodBinding name=variant163 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_194.g.vcf)]), (RodBindingCollection [(RodBinding name=variant164 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_20.g.vcf)]), (RodBindingCollection [(RodBinding name=variant165 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_200.g.vcf)]), (RodBindingCollection [(RodBinding name=variant166 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_204.g.vcf)]), (RodBindingCollection [(RodBinding name=variant167 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_207.g.vcf)]), (RodBindingCollection [(RodBinding name=variant168 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_209.g.vcf)]), (RodBindingCollection [(RodBinding name=variant169 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_21.g.vcf)]), (RodBindingCollection [(RodBinding name=variant170 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_216.g.vcf)]), (RodBindingCollection [(RodBinding name=variant171 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_217.g.vcf)]), (RodBindingCollection [(RodBinding name=variant172 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_220.g.vcf)]), (RodBindingCollection [(RodBinding name=variant173 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_229.g.vcf)]), (RodBindingCollection [(RodBinding name=variant174 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_231.g.vcf)]), (RodBindingCollection [(RodBinding name=variant175 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_232.g.vcf)]), (RodBindingCollection [(RodBinding name=variant176 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_233.g.vcf)]), (RodBindingCollection [(RodBinding name=variant177 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_24.g.vcf)]), (RodBindingCollection [(RodBinding name=variant178 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_240.g.vcf)]), (RodBindingCollection [(RodBinding name=variant179 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_241.g.vcf)]), (RodBindingCollection [(RodBinding name=variant180 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_245.g.vcf)]), (RodBindingCollection [(RodBinding name=variant181 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_26.g.vcf)]), (RodBindingCollection [(RodBinding name=variant182 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_266.g.vcf)]), (RodBindingCollection [(RodBinding name=variant183 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_267.g.vcf)]), (RodBindingCollection [(RodBinding name=variant184 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_27.g.vcf)]), (RodBindingCollection [(RodBinding name=variant185 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_281.g.vcf)]), (RodBindingCollection [(RodBinding name=variant186 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_286.g.vcf)]), (RodBindingCollection [(RodBinding name=variant187 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_29.g.vcf)]), (RodBindingCollection [(RodBinding name=variant188 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_296.g.vcf)]), (RodBindingCollection [(RodBinding name=variant189 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_300.g.vcf)]), (RodBindingCollection [(RodBinding name=variant190 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_313.g.vcf)]), (RodBindingCollection [(RodBinding name=variant191 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_314.g.vcf)]), (RodBindingCollection [(RodBinding name=variant192 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_318.g.vcf)]), (RodBindingCollection [(RodBinding name=variant193 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_32.g.vcf)]), (RodBindingCollection [(RodBinding name=variant194 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_320.g.vcf)]), (RodBindingCollection [(RodBinding name=variant195 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_325.g.vcf)]), (RodBindingCollection [(RodBinding name=variant196 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_330.g.vcf)]), (RodBindingCollection [(RodBinding name=variant197 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_340.g.vcf)]), (RodBindingCollection [(RodBinding name=variant198 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_345.g.vcf)]), (RodBindingCollection [(RodBinding name=variant199 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_354.g.vcf)]), (RodBindingCollection [(RodBinding name=variant200 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_42.g.vcf)]), (RodBindingCollection [(RodBinding name=variant201 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_44.g.vcf)]), (RodBindingCollection [(RodBinding name=variant202 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_47.g.vcf)]), (RodBindingCollection [(RodBinding name=variant203 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_48.g.vcf)]), (RodBindingCollection [(RodBinding name=variant204 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_59.g.vcf)]), (RodBindingCollection [(RodBinding name=variant205 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_65.g.vcf)]), (RodBindingCollection [(RodBinding name=variant206 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_68.g.vcf)]), (RodBindingCollection [(RodBinding name=variant207 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_73.g.vcf)]), (RodBindingCollection [(RodBinding name=variant208 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_74.g.vcf)]), (RodBindingCollection [(RodBinding name=variant209 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_76.g.vcf)]), (RodBindingCollection [(RodBinding name=variant210 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_77.g.vcf)]), (RodBindingCollection [(RodBinding name=variant211 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_78.g.vcf)]), (RodBindingCollection [(RodBinding name=variant212 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_79.g.vcf)]), (RodBindingCollection [(RodBinding name=variant213 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_81.g.vcf)]), (RodBindingCollection [(RodBinding name=variant214 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_82.g.vcf)]), (RodBindingCollection [(RodBinding name=variant215 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_83.g.vcf)]), (RodBindingCollection [(RodBinding name=variant216 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_91.g.vcf)]), (RodBindingCollection [(RodBinding name=variant217 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_92.g.vcf)]), (RodBindingCollection [(RodBinding name=variant218 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_95.g.vcf)]), (RodBindingCollection [(RodBinding name=variant219 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_97.g.vcf)]), (RodBindingCollection [(RodBinding name=variant220 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/04_99.g.vcf)]), (RodBindingCollection [(RodBinding name=variant221 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_04.g.vcf)]), (RodBindingCollection [(RodBinding name=variant222 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_05.g.vcf)]), (RodBindingCollection [(RodBinding name=variant223 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_06.g.vcf)]), (RodBindingCollection [(RodBinding name=variant224 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_07.g.vcf)]), (RodBindingCollection [(RodBinding name=variant225 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_08.g.vcf)]), (RodBindingCollection [(RodBinding name=variant226 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_09.g.vcf)]), (RodBindingCollection [(RodBinding name=variant227 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_10.g.vcf)]), (RodBindingCollection [(RodBinding name=variant228 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_101.g.vcf)]), (RodBindingCollection [(RodBinding name=variant229 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_102.g.vcf)]), (RodBindingCollection [(RodBinding name=variant230 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_103.g.vcf)]), (RodBindingCollection [(RodBinding name=variant231 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_104.g.vcf)]), (RodBindingCollection [(RodBinding name=variant232 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_105.g.vcf)]), (RodBindingCollection [(RodBinding name=variant233 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/05_64.g.vcf)]), (RodBindingCollection [(RodBinding name=variant234 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/06_05.g.vcf)]), (RodBindingCollection [(RodBinding name=variant235 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_06.g.vcf)]), (RodBindingCollection [(RodBinding name=variant236 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_07.g.vcf)]), (RodBindingCollection [(RodBinding name=variant237 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_13.g.vcf)]), (RodBindingCollection [(RodBinding name=variant238 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_14.g.vcf)]), (RodBindingCollection [(RodBinding name=variant239 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_16.g.vcf)]), (RodBindingCollection [(RodBinding name=variant240 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_17.g.vcf)]), (RodBindingCollection [(RodBinding name=variant241 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_18.g.vcf)]), (RodBindingCollection [(RodBinding name=variant242 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_20.g.vcf)]), (RodBindingCollection [(RodBinding name=variant243 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_21.g.vcf)]), (RodBindingCollection [(RodBinding name=variant244 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_23.g.vcf)]), (RodBindingCollection [(RodBinding name=variant245 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_24.g.vcf)]), (RodBindingCollection [(RodBinding name=variant246 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_25.g.vcf)]), (RodBindingCollection [(RodBinding name=variant247 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_26.g.vcf)]), (RodBindingCollection [(RodBinding name=variant248 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_27.g.vcf)]), (RodBindingCollection [(RodBinding name=variant249 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_32.g.vcf)]), (RodBindingCollection [(RodBinding name=variant250 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_33.g.vcf)]), (RodBindingCollection [(RodBinding name=variant251 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_36.g.vcf)]), (RodBindingCollection [(RodBinding name=variant252 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_37.g.vcf)]), (RodBindingCollection [(RodBinding name=variant253 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_38.g.vcf)]), (RodBindingCollection [(RodBinding name=variant254 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_39.g.vcf)]), (RodBindingCollection [(RodBinding name=variant255 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_40.g.vcf)]), (RodBindingCollection [(RodBinding name=variant256 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_42.g.vcf)]), (RodBindingCollection [(RodBinding name=variant257 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_47.g.vcf)]), (RodBindingCollection [(RodBinding name=variant258 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_48.g.vcf)]), (RodBindingCollection [(RodBinding name=variant259 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_49.g.vcf)]), (RodBindingCollection [(RodBinding name=variant260 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_50.g.vcf)]), (RodBindingCollection [(RodBinding name=variant261 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_51.g.vcf)]), (RodBindingCollection [(RodBinding name=variant262 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_52.g.vcf)]), (RodBindingCollection [(RodBinding name=variant263 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/07_54.g.vcf)]), (RodBindingCollection [(RodBinding name=variant264 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/09_02.g.vcf)]), (RodBindingCollection [(RodBinding name=variant265 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/09_03.g.vcf)]), (RodBindingCollection [(RodBinding name=variant266 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/09_07.g.vcf)]), (RodBindingCollection [(RodBinding name=variant267 source=/home/lsturm/projects1/elite/bcbio/projects/project_n268_gatk/09_08.g.vcf)])] out=/scratch/PI/euan/projects/elite/bcbio/projects/project_n267_gatk_joint/elite_n267_joint.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= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> | |
| ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.6-0-g89b7209,Date="Wed Aug 24 01:12:39 PDT 2016",Epoch=1472026359907,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/home/lsturm/projects1/elite/genotype/bams/04_266/04_266.bam] 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=/home/lsturm/apps/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.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=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 likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, AS_Standard] 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"> | |
| ##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=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=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient"> | |
| ##INFO=<ID=AS_QD,Number=1,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth"> | |
| ##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities"> | |
| ##INFO=<ID=AS_RAW_MQ,Number=A,Type=Float,Description="Allele-specfic raw data for RMS Mapping Quality"> | |
| ##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specific raw data for Mapping Quality Rank Sum"> | |
| ##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias"> | |
| ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests"> | |
| ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> | |
| ##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=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"> | |
| ##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> | |
| ##contig=<ID=GL000207.1,length=4262> | |
| ##contig=<ID=GL000226.1,length=15008> | |
| ##contig=<ID=GL000229.1,length=19913> | |
| ##contig=<ID=GL000231.1,length=27386> | |
| ##contig=<ID=GL000210.1,length=27682> | |
| ##contig=<ID=GL000239.1,length=33824> | |
| ##contig=<ID=GL000235.1,length=34474> | |
| ##contig=<ID=GL000201.1,length=36148> | |
| ##contig=<ID=GL000247.1,length=36422> | |
| ##contig=<ID=GL000245.1,length=36651> | |
| ##contig=<ID=GL000197.1,length=37175> | |
| ##contig=<ID=GL000203.1,length=37498> | |
| ##contig=<ID=GL000246.1,length=38154> | |
| ##contig=<ID=GL000249.1,length=38502> | |
| ##contig=<ID=GL000196.1,length=38914> | |
| ##contig=<ID=GL000248.1,length=39786> | |
| ##contig=<ID=GL000244.1,length=39929> | |
| ##contig=<ID=GL000238.1,length=39939> | |
| ##contig=<ID=GL000202.1,length=40103> | |
| ##contig=<ID=GL000234.1,length=40531> | |
| ##contig=<ID=GL000232.1,length=40652> | |
| ##contig=<ID=GL000206.1,length=41001> | |
| ##contig=<ID=GL000240.1,length=41933> | |
| ##contig=<ID=GL000236.1,length=41934> | |
| ##contig=<ID=GL000241.1,length=42152> | |
| ##contig=<ID=GL000243.1,length=43341> | |
| ##contig=<ID=GL000242.1,length=43523> | |
| ##contig=<ID=GL000230.1,length=43691> | |
| ##contig=<ID=GL000237.1,length=45867> | |
| ##contig=<ID=GL000233.1,length=45941> | |
| ##contig=<ID=GL000204.1,length=81310> | |
| ##contig=<ID=GL000198.1,length=90085> | |
| ##contig=<ID=GL000208.1,length=92689> | |
| ##contig=<ID=GL000191.1,length=106433> | |
| ##contig=<ID=GL000227.1,length=128374> | |
| ##contig=<ID=GL000228.1,length=129120> | |
| ##contig=<ID=GL000214.1,length=137718> | |
| ##contig=<ID=GL000221.1,length=155397> | |
| ##contig=<ID=GL000209.1,length=159169> | |
| ##contig=<ID=GL000218.1,length=161147> | |
| ##contig=<ID=GL000220.1,length=161802> | |
| ##contig=<ID=GL000213.1,length=164239> | |
| ##contig=<ID=GL000211.1,length=166566> | |
| ##contig=<ID=GL000199.1,length=169874> | |
| ##contig=<ID=GL000217.1,length=172149> | |
| ##contig=<ID=GL000216.1,length=172294> | |
| ##contig=<ID=GL000215.1,length=172545> | |
| ##contig=<ID=GL000205.1,length=174588> | |
| ##contig=<ID=GL000219.1,length=179198> | |
| ##contig=<ID=GL000224.1,length=179693> | |
| ##contig=<ID=GL000223.1,length=180455> | |
| ##contig=<ID=GL000195.1,length=182896> | |
| ##contig=<ID=GL000212.1,length=186858> | |
| ##contig=<ID=GL000222.1,length=186861> | |
| ##contig=<ID=GL000200.1,length=187035> | |
| ##contig=<ID=GL000193.1,length=189789> | |
| ##contig=<ID=GL000194.1,length=191469> | |
| ##contig=<ID=GL000225.1,length=211173> | |
| ##contig=<ID=GL000192.1,length=547496> | |
| ##reference=file:///home/lsturm/apps/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa | |
| ##bcftools_viewVersion=1.3+htslib-1.3 | |
| ##bcftools_viewCommand=view -h bcbio/projects/project_n267_gatk_joint/elite_n267_joint.vcf | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 01_02 01_03 01_05 01_06 01_07 01_08 01_09 01_10 01_11 01_12 01_14 01_15 01_16 01_17 01_18 01_19 01_25 01_26 01_27 01_28 01_29 01_30 01_32 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 01_63 01_64 01_67 01_68 01_71 01_72 01_73 01_75 01_76 02_01 02_02 02_03 02_04 02_06 02_14 02_15 02_17 02_19 02_21 02_23 02_27 02_29 02_30 02_34 02_35 02_36 02_39 03_01 03_02 03_03 03_04 03_05 03_06 03_07 03_08 03_09 03_11 03_12 03_13 03_14 03_15 03_16 03_17 03_18 03_19 03_20 03_21 03_22 03_23 03_24 03_25 03_26 03_27 03_28 03_29 03_30_102A 03_31 03_32 03_33 03_35 03_36 03_37 03_38 03_39 03_41 03_42 03_43 03_44 03_45 03_47 03_49 03_51 03_54 03_55 03_56 03_57 03_58 03_60 03_61 03_63 03_64 03_65 03_66_101a 03_67_105a 03_68_10_03 03_71 03_72 03_73 03_75 03_76 03_77 03_78 03_92 03_93 04_04 04_06 04_09 04_106 04_107 04_109 04_110 04_119 04_122 04_123 04_124 04_125 04_126 04_127 04_13 04_14 04_145 04_147 04_150 04_153 04_157 04_16 04_164 04_165 04_171 04_172 04_174 04_178 04_18 04_185 04_192 04_194 04_20 04_200 04_204 04_207 04_209 04_21 04_216 04_217 04_220 04_229 04_231 04_232 04_233 04_24 04_240 04_241 04_245 04_26 04_266 04_267 04_27 04_281 04_286 04_29 04_296 04_300 04_313 04_314 04_318 04_32 04_320 04_325 04_330 04_340 04_345 04_354 04_42 04_44 04_47 04_48 04_59 04_65 04_68 04_73 04_74 04_76 04_77 04_78 04_79 04_81 04_82 04_83 04_91 04_92 04_95 04_97 04_99 05_04 05_05 05_06 05_07 05_08 05_09 05_10 05_101 05_102 05_103 05_104 05_105 05_64 06_05 07_06 07_07 07_13 07_14 07_16 07_17 07_18 07_20 07_21 07_23 07_24 07_25 07_26 07_27 07_32 07_33 07_36 07_37 07_38 07_39 07_40 07_42 07_47 07_48 07_49 07_50 07_51 07_52 07_54 09_02 09_03 09_07 09_08 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment