stats file in Mutect2 calling

Question

[dentepre]

Hi,

I'm performing somatic variant calling with Mutect2. However, besides the *.vcf file, the stats file is not generated.

The Genome Analysis Toolkit (GATK) v4.1.2.0 HTSJDK Version: 2.19.0 Picard Version: 2.19.0

gatk Mutect2 -R hg38.fa -I normal.bam --normal normal -I tumour.bam --tumor tumour -O results/mutect/summary.vcf

Where is my mistake? How can I force to generate stats file?

Answer 1

[vipulbhatia24]

Hello,

I also encountered the same problem. Were you able to resolve this?

If someone can help please.

Answer 2

[aldhairmedico]

This thread may be useful for you: https://gatk.broadinstitute.org/hc/en-us/community/posts/360068479891-Mutect2-doesn-t-produce-stats-file