[GATK version used - v18.104.22.168]
I have germline and somatic variants called using HaplotypeCaller and Mutect2. As you can see from the title of the posting, it was done using tumor samples without matched normals.
I was wondering what would be "best" (since matched normal would be actually best) approach to filter out false positive calls from Mutect2. My plan originally was to first filter out any variants in germline and somatic calls that overlap, if there are any.
Would it be better to look into other tools that specializes in looking for somatic variants when only tumor samples are available?
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