How can I call SNPs from mapped reads (bwa-mem, hg38) with mapping quality MAPQ value zero using GATK4 (v18.104.22.168) Mutect2?
I already tried to disable all the read filters one by one with --disable-read-filter but I got an error and Mutect2 doesn't work. I also used --disable-tool-default-read-filters true but I got the same error.
I know that you don't recommend disabling filters but I need to call somatic variants on a specific genes with multi-mapped issues that is frequently mutated in cancer.
Thanks for your help.
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