How to force MuTect2 genotype all sites within intervals?
I cannot generate genotypes for all input sites with MuTect2 (-L input.vcf). I tried --output_mode EMIT_ALL_SITES and -gt_mode GENOTYPE_GIVEN_ALLELES without luck. Is there an equivalent option to --force_output in MuTect? I know it is more complicated with indels where it is not applicable to generate all possible indels, but I am only interested in the specific genotypes I used with -L.