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pjotrp

Expanded the VCF header parser to accommodate GATK

Feb 14, 2015

04b8935 · Feb 14, 2015

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{ "HEADER": { "files": [], }, "COLUMNS": ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT","Original","s1t1","s2t1","s3t1","s1t2","s2t2","s3t2"], "META": {"INFO":{"AC":{"ID":"AC","Number":"A","Type":"Integer","Description":"Allele count in genotypes, for each ALT allele, in the same order as listed"},"AF":{"ID":"AF","Number":"A","Type":"Float","Description":"Allele Frequency, for each ALT allele, in the same order as listed"},"AN":{"ID":"AN","Number":"1","Type":"Integer","Description":"Total number of alleles in called genotypes"},"BaseQRankSum":{"ID":"BaseQRankSum","Number":"1","Type":"Float","Description":"Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"},"DP":{"ID":"DP","Number":"1","Type":"Integer","Description":"Approximate read depth; some reads may have been filtered"},"DS":{"ID":"DS","Number":"0","Type":"Flag","Description":"Were any of the samples downsampled?"},"Dels":{"ID":"Dels","Number":"1","Type":"Float","Description":"Fraction of Reads Containing Spanning Deletions"},"FS":{"ID":"FS","Number":"1","Type":"Float","Description":"Phred-scaled p-value using Fisher's exact test to detect strand bias"},"HaplotypeScore":{"ID":"HaplotypeScore","Number":"1","Type":"Float","Description":"Consistency of the site with at most two segregating haplotypes"},"InbreedingCoeff":{"ID":"InbreedingCoeff","Number":"1","Type":"Float","Description":"Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"},"MLEAC":{"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"},"MLEAF":{"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"},"MQ":{"ID":"MQ","Number":"1","Type":"Float","Description":"RMS Mapping Quality"},"MQ0":{"ID":"MQ0","Number":"1","Type":"Integer","Description":"Total Mapping Quality Zero Reads"},"MQRankSum":{"ID":"MQRankSum","Number":"1","Type":"Float","Description":"Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"},"QD":{"ID":"QD","Number":"1","Type":"Float","Description":"Variant Confidence/Quality by Depth"},"RPA":{"ID":"RPA","Number":".","Type":"Integer","Description":"Number of times tandem repeat unit is repeated, for each allele (including reference)"},"RU":{"ID":"RU","Number":"1","Type":"String","Description":"Tandem repeat unit 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Jan 25 10:33:56 CET 2014","Epoch":1390642436187,"CommandLineOptions":"analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 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 output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) 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 onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"}},"fileformat":"VCFv4.1","reference":"file:human_g1k_v37.fasta"}, "BODY": [ { "seq:chr": "1" , "seq:pos": 10257 , "seq:ref": "A" , "seq:alt": "C" , "dp": 1518 , "samples" : { "Original": { "AD": [151,8], "DP": 159, "GQ": 99, "GT": "0/0", "PL": [0,195,2282] } , "s1t1": { "AD": [219,22], "DP": 242, "GQ": 99, "GT": "0/0", "PL": [0,197,2445] } , "s2t1": { "AD": [227,22], "DP": 249, "GQ": 90, "GT": "0/0", "PL": [0,90,2339] } , "s3t1": { "AD": [226,22], "DP": 249, "GQ": 99, "GT": "0/0", "PL": [0,159,2695] } , "s1t2": { "AD": [166,18], "DP": 186, "GQ": 99, "GT": "0/0", "PL": [0,182,1989] } , "s2t2": { "AD": [185,27], "DP": 212, "GQ": 99, "GT": "0/1", "PL": [111,0,2387] } , "s3t2": { "AD": [201,15], "DP": 218, "GQ": 24, "GT": "0/0", "PL": [0,24,1972] } } }, { "seq:chr": "1" , "seq:pos": 10291 , "seq:ref": "C" , "seq:alt": "T" , "dp": 1433 , "samples" : { "Original": { "AD": [145,16], "DP": 165, "GQ": 23, "GT": "0/1", "PL": [23,0,491] } , "s1t1": { "AD": [218,26], "DP": 249, "GQ": 29, "GT": "0/1", "PL": [29,0,611] } , "s2t1": { "AD": [214,30], "DP": 249, "GQ": 99, "GT": "0/1", "PL": [145,0,801] } , "s3t1": { "AD": [213,32], "DP": 247, "GQ": 20, "GT": "0/1", "PL": [20,0,1031] } , "s1t2": { "AD": [122,36], "DP": 161, "GQ": 99, "GT": "0/1", "PL": [347,0,182] } , "s2t2": { "AD": [131,27], "DP": 163, "GQ": 99, "GT": "0/1", "PL": [255,0,508] } , "s3t2": { "AD": [156,31], "DP": 189, "GQ": 99, "GT": "0/1", "PL": [252,0,372] } } }, { "seq:chr": "1" , "seq:pos": 10297 , "seq:ref": "C" , "seq:alt": "T" , "dp": 1440 , "samples" : { "Original": { "AD": [155,18], "DP": 182, "GQ": 44, "GT": "0/1", "PL": [44,0,654] } , "s1t1": { "AD": [218,23], "DP": 246, "GQ": 21, "GT": "0/1", "PL": [21,0,673] } , "s2t1": { "AD": [219,26], "DP": 250, "GQ": 41, "GT": "0/1", "PL": [41,0,898] } , "s3t1": { "AD": [207,30], "DP": 246, "GQ": 39, "GT": "0/0", "PL": [0,39,963] } , "s1t2": { "AD": [137,20], "DP": 165, "GQ": 21, "GT": "0/0", "PL": [0,21,363] } , "s2t2": { "AD": [124,27], "DP": 158, "GQ": 65, "GT": "0/1", "PL": [65,0,435] } , "s3t2": { "AD": [151,27], "DP": 183, "GQ": 63, "GT": "0/1", "PL": [63,0,485] } } }, { "seq:chr": "1" , "seq:pos": 10303 , "seq:ref": "C" , "seq:alt": "T" , "dp": 1460 , "samples" : { "Original": { "AD": [169,25], "DP": 198, "GQ": 99, "GT": "0/1", "PL": [195,0,609] } , "s1t1": { "AD": [211,31], "DP": 247, "GQ": 1, "GT": "0/1", "PL": [1,0,656] } , "s2t1": { "AD": [214,28], "DP": 248, "GQ": 7, "GT": "0/0", "PL": [0,7,982] } , "s3t1": { "AD": [214,32], "DP": 248, "GQ": 25, "GT": "0/0", "PL": [0,25,980] } , "s1t2": { "AD": [146,17], "DP": 172, "GQ": 2, "GT": "0/0", "PL": [0,2,353] } , "s2t2": { "AD": [123,23], "DP": 157, "GQ": 17, "GT": "0/1", "PL": [17,0,541] } , "s3t2": { "AD": [156,22], "DP": 182, "GQ": 19, "GT": "0/0", "PL": [0,19,413] } } }, { "seq:chr": "1" , "seq:pos": 10315 , "seq:ref": "C" , "seq:alt": "T" , "dp": 1500 , "samples" : { "Original": { "AD": [181,26], "DP": 212, "GQ": 41, "GT": "0/1", "PL": [41,0,618] } , "s1t1": { "AD": [223,17], "DP": 246, "GQ": 99, "GT": "0/0", "PL": [0,102,832] } , "s2t1": { "AD": [219,20], "DP": 242, "GQ": 66, "GT": "0/0", "PL": [0,66,924] } , "s3t1": { "AD": [217,23], "DP": 245, "GQ": 99, "GT": "0/0", "PL": [0,109,1384] } , "s1t2": { "AD": [155,27], "DP": 190, "GQ": 97, "GT": "0/1", "PL": [97,0,328] } , "s2t2": { "AD": [130,20], "DP": 157, "GQ": 10, "GT": "0/1", "PL": [10,0,531] } , "s3t2": { "AD": [163,24], "DP": 189, "GQ": 5, "GT": "0/0", "PL": [0,5,450] } } }, { "seq:chr": "1" , "seq:pos": 10321 , "seq:ref": "C" , "seq:alt": "T" , "dp": 1537 , "samples" : { "Original": { "AD": [189,25], "DP": 218, "GQ": 30, "GT": "0/1", "PL": [30,0,810] } , "s1t1": { "AD": [219,22], "DP": 246, "GQ": 24, "GT": "0/0", "PL": [0,24,593] } , "s2t1": { "AD": [218,27], "DP": 248, "GQ": 34, "GT": "0/1", "PL": [34,0,1134] } , "s3t1": { "AD": [220,22], 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