SOLVED: Get read counts of Mutect2 somatic variants

Follow

Mariana E. M.

• August 11, 2023 15:17
• Edited

Dear GATK community,

I performed short somatic variant calling with Mutect2 - what would be the best way of getting the read count for every detected variant?
I want to get both the number of reads that contains the detected variant as well as the total number of reads covering that locus.

Is there a GATK tool I could use for this?

Many thanks in advance.

1

• 

  Mariana E. M.

  • August 11, 2023 15:16

  SOLVED:

  I realized that this information is actually contained in the VCF file as allele depth (AD), reporting the number of reads supporting the reference and alternative allele. The identifier (AD) is in the column "FORMAT" and its value in the subsequent column.

  Details can also be found in the GATK documentation about VCF files.

  1

  Comment actions Permalink

Please sign in to leave a comment.