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Fix GenotypeGVCFs bug for variants with zero or no INFO DP (#7491)
Catch corner case for DP=0/no DP variants Clean up raw annotations for AS_QD
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src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/homVar1DP.g.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| ##fileformat=VCFv4.2 | ||
| ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> | ||
| ##FILTER=<ID=LowQual,Description="Low quality"> | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##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=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> | ||
| ##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path genomicsdb --batch-size 50 --consolidate true --sample-name-map /cromwell_root/broad-gotc-test-storage/joint_genotyping/exome/plumbing/callset/reblocked_name_sample_map --merge-input-intervals true --reader-threads 5 --intervals /cromwell_root/broad-gotc-dev-cromwell-execution/JointGenotyping/0deab674-7c38-4a93-a511-51c65b5b991c/call-SplitIntervalList/glob-d928cd0f5fb17b6bd5e635f48c18ccfb/0002-scattered.interval_list --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --validate-sample-name-map false --max-num-intervals-to-import-in-parallel 1 --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.0",Date="September 25, 2020 4:12:49 PM GMT"> | ||
| ##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output homVarNoDP.g.vcf --call-genotypes true --variant gendb://genomicsdb --intervals chr4:189917428 --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.2.2.0-3-gc1f3737-SNAPSHOT",Date="October 4, 2021 11:09:18 AM EDT"> | ||
| ##GVCFBlock0-10=minGQ=0(inclusive),maxGQ=10(exclusive) | ||
| ##GVCFBlock10-20=minGQ=10(inclusive),maxGQ=20(exclusive) | ||
| ##GVCFBlock20-30=minGQ=20(inclusive),maxGQ=30(exclusive) | ||
| ##GVCFBlock30-40=minGQ=30(inclusive),maxGQ=40(exclusive) | ||
| ##GVCFBlock40-50=minGQ=40(inclusive),maxGQ=50(exclusive) | ||
| ##GVCFBlock50-60=minGQ=50(inclusive),maxGQ=60(exclusive) | ||
| ##GVCFBlock60-100=minGQ=60(inclusive),maxGQ=100(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_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities"> | ||
| ##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele"> | ||
| ##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_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality"> | ||
| ##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum"> | ||
| ##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth"> | ||
| ##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations"> | ||
| ##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=1,Type=String,Description="Allele-specfic raw data for RMS Mapping Quality"> | ||
| ##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specfic 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_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref 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=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias"> | ||
| ##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes; effectively sum of ADs"> | ||
| ##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=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=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=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=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead."> | ||
| ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> | ||
| ##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score"> | ||
| ##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity"> | ||
| ##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation."> | ||
| ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | ||
| ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> | ||
| ##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes"> | ||
| ##contig=<ID=chr4,length=190214555,assembly=Homo_sapiens_assembly38.fasta.gz> | ||
| ##reference=file:///Users/gauthier/workspaces/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz | ||
| ##source=GenomicsDBImport | ||
| ##source=SelectVariants | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CHMI_CHMI3_Nex1 NA12878 NA12891 NA12892 NA19238 NA20845 NA20846 NA20847 NA20849 NA20850 NA20851 NA20852 NA20853 NA20854 NA20856 NA20858 NA20859 NA20861 NA20862 NA20866 NA20869 NA20870 NA20871 NA20872 NA20873 NA20874 NA20875 NA20876 NA20877 NA20878 NA20881 NA20885 NA20886 NA20887 NA20888 NA20889 NA20890 NA20891 NA20892 NA20893 NA20894 NA20895 NA20896 NA20897 NA20898 NA20899 NA20901 NA20902 NA20903 NA20904 NA20905 NA20906 NA20908 NA20910 NA20911 NA21086 NA21087 NA21088 NA21093 NA21095 NA21114 NA21124 NA21126 NA21129 NA21137 | ||
| chr4 189917428 . C G,<NON_REF> . . AS_QUALapprox=|45|;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.000|0.000|0.000;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;MQ_DP=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=0,0;VarDP=1 GT:AD:GQ:PGT:PID:PL:SB:DP .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. 1/1:0,0,0:3:0|1:189917424_A_G:45,3,0,45,3,45:0,0,0,0:0 .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. |
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