MuTect2 gives only a vcf file as output. For MuTect, we have 4 files generated for each sample:
B62047_N018_call_stats.out B62047_N018_coverage.wig.txt B62047_N018.vcf B62047_N018.vcf.idx
I know how to work with MuTect output for Onctator annotation, and filtering with qualities.
But only from vcf that MuTect2 gives, how can we do any sort of filtering?