REQUIRED for all errors and issues:
a) GATK version used: v22.214.171.124
b) Exact command used:gatk --java-options "-Xms50G -Xmx70G" Mutect2 -R $REF -I Tumor1.bam --tumor-sample Tumor1 -I Normal.bam --normal-sample Normal1 -O Raw.vcf
c) Entire program log:
After my successful Mutect2 run, out VCF file contains /shows variants in Tumor sample as well as Normal sample.
It should only contains/show variants in Tumor sample and Normal variants should be filtered out,
I am interested in variants found in Tumor (not in matched normal).
My question is :
1. Why Mutect2 output VCF shows variants found in both (Normal and Tumor) samples ?
2. How should I get variants found uniquely in Tumor (not in matched Nromal) ?
Thanks in advanced.
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