Mutect2 -could not detect expected Indels

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Shivangi Agarwal

• August 21, 2023 17:45

REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

Hi GATK team,

I am calling somatic variants using Mutect2 for 10 samples. I could see lots of missense mutations but could not find expected small Indels there in all 10 samples. What may be the reason ? I think Mutect2 is able to detect both SNVs and Indels well. Please clarify and let me know if I need to tweak some parameters.

a) GATK version used: 4.2.2.0

b) Exact command: python3 gatk mutect2 -R hg19.fasta -I sample1.bam --max-mnp-distance 0 -o sample1.vcf.gz.

 

 

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  Gökalp Çelik

  • August 24, 2023 16:00

  Hi Shivangi Agarwal

  Mutect2 and HaplotypeCaller of GATK utilizes local reassembly for genotyping of variants and the default parameters of both tools are mostly optimized for whole genome and exome sequencing samples and therefore may not be enough for other special NGS data types such as amplicon sequencing. Depth of data may also be an issue for some variants however these tools have bunch of parameters for tuning for those cases and some of the most useful parameters are summarized in the following article 

  https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant 

  Can you try some of the recommended tunable parameters and let us know whether that works for you? 

  Regards. 

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  Shivangi Agarwal

  • August 29, 2023 14:28

  Okay, thanks. I am looking into it and will get back to you soon.

   

   

   

  Thanks,

  Shivangi

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