-
Notifications
You must be signed in to change notification settings - Fork 575
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
fixing bugs in CalculateGenotypePosteriers
fixing 3 issues in CalclualteGenotypePosteriers * no longer emit duplicate variants if you have overlapping VCF records in the input * specifying vcf.gz output will produce a vcf.gz instead of an unzipped file called vcf.gz * fix potential NPE during shutdown
- Loading branch information
1 parent
2efffce
commit fa09fce
Showing
4 changed files
with
156 additions
and
44 deletions.
There are no files selected for viewing
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
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
50 changes: 50 additions & 0 deletions
50
...s/variantutils/CalculateGenotypePosteriors/overlappingVariants.expected.no_duplicates.vcf
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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| ##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 |
Oops, something went wrong.