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fixing bugs in CalculateGenotypePosteriers #4352
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6 changes: 6 additions & 0 deletions
6
...ellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/badMLEAC_count_not_A.vcf
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##fileformat=VCFv4.2 | ||
##INFO=<ID=MLEAC,Number=R,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"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##contig=<ID=chr1,length=248956422> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT USH_C1 USH_F1 USH_M1 | ||
chr1 3872413 . AG A 400.09 PASS MLEAC=1 GT 0/0 0/0 0/1 |
6 changes: 6 additions & 0 deletions
6
...llbender/tools/walkers/variantutils/CalculateGenotypePosteriors/badMLEAC_type_not_int.vcf
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##fileformat=VCFv4.2 | ||
##INFO=<ID=MLEAC,Number=A,Type=Float,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"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##contig=<ID=chr1,length=248956422> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT USH_C1 USH_F1 USH_M1 | ||
chr1 3872413 . AG A 400.09 PASS MLEAC=1 GT 0/0 0/0 0/1 |
5 changes: 5 additions & 0 deletions
5
...stitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/noGenotypes.vcf
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##fileformat=VCFv4.2 | ||
##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"> | ||
##contig=<ID=chr1,length=248956422> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO | ||
chr1 3872413 . AG A 400.09 PASS MLEAC=1 |
50 changes: 50 additions & 0 deletions
50
...s/variantutils/CalculateGenotypePosteriors/overlappingVariants.expected.no_duplicates.vcf
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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=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -2.4321 <= x < -0.3748"> | ||
##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -103.9799"> | ||
##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -103.9799 <= x < -2.4321"> | ||
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -6.7044 <= x < -0.2206"> | ||
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -3000.6876"> | ||
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -3000.6876 <= x < -6.7044"> | ||
##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=PP,Number=G,Type=Integer,Description="Phred-scaled Posterior Genotype Probabilities"> | ||
##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=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /media/md1200/analysis/Case/Chen_ming/171031/USH_trio.indel.recal --tranches-file USH_trio.indel.tranches --output USH_trio.recal.vcf.gz --truth-sensitivity-filter-level 99.0 --mode INDEL --variant USH_trio.snp.recal.vcf.gz --reference /media/md1200/ref/hsa/genome/GRCh38/fasta/Homo_sapiens_assembly38.fasta --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered 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 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.0.0,Date="January 22, 2018 4:59:11 PM CST"> | ||
##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=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> | ||
##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=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=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=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants"> | ||
##INFO=<ID=PG,Number=G,Type=Integer,Description="Genotype Likelihood Prior"> | ||
##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=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"> | ||
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds 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"> | ||
##contig=<ID=chr1,length=248956422> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT USH_C1 USH_F1 USH_M1 | ||
chr1 3872413 . AG A 400.09 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.760e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;PG=0,0,0;QD=10.53;ReadPosRankSum=-1.513e+00;SOR=0.787;VQSLOD=4.73;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:PP 0/0:27,0:27:81:0,81,712:0,81,712 0/0:45,0:45:99:0,111,1665:0,111,1665 0/1:17,21:38:99:440,0,469:440,0,469 | ||
chr1 3872414 . GA G 29.18 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=0.246;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.167;MQ=76.93;MQRankSum=0.00;PG=0,0,0;QD=0.50;ReadPosRankSum=0.352;SOR=0.472;VQSLOD=3.93;culprit=QD GT:AD:DP:GQ:PL:PP 0/0:29,0:29:16:0,16,666:0,16,666 0/1:48,10:58:69:69,0,1051:69,0,1051 0/0:35,3:38:54:0,54,912:0,54,912 |
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Oops, this should probably be builder2, right? All this time and no one ever said anything.
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It definitely looks like it should be. It's effectively the same thing, but it's very confusing and if anyone ever make changes it could lead to problems... I might start a separate PR to address that.
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wait, what am I talking about... the thing that gets output should be the the result of modifying builder2 and we modify builder. That seems super wrong.
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no, i'm back to "it's dumb but fine"
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new pr to fix this #4431