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: 220.127.116.11
b) Exact command: python3 gatk mutect2 -R hg19.fasta -I sample1.bam --max-mnp-distance 0 -o sample1.vcf.gz.
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