If not an error, choose a category for your question(REQUIRED):
c) Why do I see a large number of false positive (especially germlines) after calling somatic variants by Mutect2?
d) Where do I find the best way to decrease false positive rates without compromising sensitivity?
I used GATK/Mutect 2 (GenomeAnalysisTk/18.104.22.168) to call somatic variants using tumor-normal pairs. The default setting was used throughout, following the best practice protocol. However, I found lots of false positives (many appear germline variants, seen in the blood as well). By quick inspection of 113 variants from the original BAMs on IGV, I found only 35% of true positive rate. For example, the following variants, which are obviously germline on IGV (source is BAM), are called as somatic.
My question are :
1) What are the known true positive rate for GATK2 (22.214.171.124)
2) Any suggestion for option arguments or filtering to remove these obvious false positives without compromising sensitivity?
3) Or am I simply doing this wrong? Any comments/suggestions are appreciated.
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