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MuTect2 amplicon somatic calling, variants missed, -stand_emit no effect
I'm trying to use MuTect2 for somatic calling between matched tumour normal pairs of amplicon sequencing.
Using the default parameters there are about 10 variants that I have reasons to believe should be called but are not called with the default parameters of mutect2.
Here is my command:
java-jar GenomeAnalysisTK.jar -T MuTect2 -I:tumor tumour.bam -I:normal normal.bam -R GRCh37-lite.fa --disable_read_filter DuplicateRead
Since there were a few missed variants I tried using the -stand_emit_conf parameter across 1-10 to see if anything should change. I got the exact same calls each time. Should I be using a different parameter to tune the sensitivity of Mutect2?