When running CloudMap unmapped mutant workflow, I get a SnpEff file with Homozygous or heterozygous status for each called variant. However I would like to have the ratio of alternate non-reference alleles / total number of alleles, to set up the threshold as I would like. Then:
-Would it be possible to have the ratio of ALT / TOT for each variant instead of « homozygous » or « heterozygous » in the homozygous field of the tabular file?
-If not, is it possible to filter the data in VCF file before running the SnpEff tool? Which expression should I use?