How do I add allele depth to Mutect2 output?

Follow

Ashi

• December 12, 2020 22:23

Tool version: GATK4.1.9.0

Sample: Whole genome sequence, human cancer.

 

I need "allelic depth" (i.e, DepthPerAlleleBySample in Haplotypecaller)information in somatic.vcf for some further analysis. I am using Mutect2 for somatic SVN calling according to current best practice for somatic SNV calling in GATK.

Haplotypecaller has function to calculate "allelic depth", but Mutect2 does not.

How do I add allelic depth to Mutect2 output vcf files? Does anyone have suggestion?

0

• 

  Genevieve Brandt (she/her)

  • December 18, 2020 17:26

  Hi Ashi,

  Thank you for your question! This question falls outside of the scope of GATK Support. (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

  0

  Comment actions Permalink
• 

  David Benjamin

  • March 03, 2021 14:06

  Ashi Mutect2 emits the AD genotype field for each sample.  Is that what you want?

  0

  Comment actions Permalink

Please sign in to leave a comment.