The missing value in Mutect2 vcf

Follow

Hsu Pei-Chun

• January 06, 2021 02:33

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

0

• 

  Genevieve Brandt (she/her)

  • January 06, 2021 20:40

  Hi Hsu Pei-Chun,

  Thank you for your question! This question falls outside of the scope of GATK Support, as it is not an error or abnormal result (See our support policy for more details). However, we encourage you to keep posting questions because they help us improve our documentation and build resources. In addition, if you know the answer to other questions outside of our GATK support team scope, please help out other users! And other users feel free to chime and discuss here.

  Mutect2 is a popular topic on the forum so we wrote an FAQ article answering many of the questions posted in the last year. Please see that article, as well as our other comprehensive documentation, in case your answer is there.

  • Mutect2 FAQ

  • Mutect2 Tool Docs

  • Mutect2 paper

  • Mutect2 in our Best Practices

  • When Mutect2 does not call an expected variant - Troubleshooting

   

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • March 02, 2021 16:58

  Hi Hsu Pei-Chun,

  There was a similar post to yours on our forum and one of our developers gave some info that might be helpful to you as well. Please see this link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360076993852-QUAL-values-not-present-in-Mutect2-VCF

  Hope this helps!

  Genevieve

  0

  Comment actions Permalink

Please sign in to leave a comment.