Individual vs. joint call VCFs
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7 months ago
Sd • 0

Is there any way to figure out and be sure if a VCF file is individually called or jointly called? Is there any line in the VCF header to look at for this?

GATK VCF WGS • 1.2k views
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I am no expert on VCF files but wouldn't a VCF file with multiple sample names in the header column tell you that it's a joint call?

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if they used bcftools to merge a bunch of gvcfs then it wouldn't be a joint genotyping in the same way GATK performs it, which leverages quality information from many samples to infer artefactual variants. Either way there should be a line in the header.

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I have GenotypeGVCFs command lines in the header of each VCFs but I am not sure whether they used bcftools or GATK tools (either CombineGVCFs or GenomicsDBImport).

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GenotypeGVCFs would indicate GATK joint genotyping was used. mystery solved.

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I'd suggest that if you see variants that fail filters in some samples, due to very low (but nonzero) allele frequency, the data was likely jointly called. Unless it's a gVCF.

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7 months ago
raphael.B ▴ 520

You may find a line in the VCF header telling you how it has been produced. If you don't , checking the genotypes might be good start. You should have a lot of no call ( and in theory no homozygous reference call) with missing classic information (like DP) that were produced during the merge.

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This is what I have for GenotypeGVCFs commands in the VCFs header:

 \ ##GATKCommandLine=<ID=GenotypeGVCFs,Version=4-3.3.0-0,Date="Thu Aug 11 00:03:52 GMT 2018",Epoch=1524096052515,CommandLineOptions="analysis_type=GenotypeGVCFs 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=/data/reference/Homo_sap/hg38/Sequence/genome_hg38.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 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=ALL 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 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=1001.PE.ra.md.g.vcf.gz)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub includeNonVariantSites=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 input_prior=[] sample_ploidy=2 annotation=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, GenotypeSummaries, StrandOddsRatio] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
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