The missing value in Mutect2 vcf
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: gatk-package-4.1.8.1-local.jar and gatk-package-4.1.2.0-local.jar
b) Exact command used:
java -jar -Xmx96G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true ~/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar Mutect2 -R ~/reference_seq/hg38/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -I sample.sorted.dedup.hg38.bam -O sample.hg38.gnomad.g1kpon.wAF.vcf -tumor sample --germline-resource somatic-hg38_af-only-gnomad.hg38.vcf.gz -pon somatic-hg38_1000g_pon.hg38.vcf.gz" --af-of-alleles-not-in-resource 0.0000025
c) Why do I see the "." value in the ID,QUAL and FILTER field in vcf file?
| #CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | sample |
| chr1 | 13504 | . | G | A | . | . | AS_SB_TABLE=24,14|14,0;DP=52;ECNT=1;MBQ=31,33;MFRL=265,279;MMQ=24,24;MPOS=38;POPAF=2.23;TLOD=25.61 | GT:AD:AF:DP:F1R2:F2R1:SB | 0/1:38,14:0.277:52:24,6:14,8:24,14,14,0 |
| chr1 | 14975 | . | C | T | . | . | AS_SB_TABLE=4,0|1,1;DP=6;ECNT=1;MBQ=35,33;MFRL=299,389;MMQ=25,33;MPOS=50;POPAF=3.10;TLOD=4.63 | GT:AD:AF:DP:F1R2:F2R1:SB | 0/1:4,2:0.375:6:2,0:2,2:4,0,1,1 |
| chr1 | 19004 | . | A | G | . | . | AS_SB_TABLE=1,0|2,0;DP=3;ECNT=1;MBQ=33,28;MFRL=291,323;MMQ=23,22;MPOS=5;POPAF=0.357;TLOD=4.27 | GT:AD:AF:DP:F1R2:F2R1:SB | 0/1:1,2:0.600:3:1,1:0,1:1,0,2,0 |
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Hi Hsu Pei-Chun, were you able to solve this issue? Your question was posted while our GATK Team was Out of Office and we did not get to your question.
If you still would like support from the GATK Team, please repost your question with [Repost] in the title and we will get to it as soon as possible.
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Hsu Pei-Chun This is the correct behavior. Mutect2 does not emit a QUAL or ID. You need to run FilterMutectCalls to get the FILTER field.
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