Python implementation of viral trimming + variant calling, similar to iVar
Usage of call_variant_fetch.py: python3 call_variant_fetch.py AlignmentFile ReferenceFile VariantOutputFilename [-q minimal quality score to count base (Default:20)] [-t minimal frequency threshold to call variant (Default:0.03)] [-m minimal number of reads to call variant (Default:0)]
Usage of call_variant_pileup.py: python3 call_variant_pileup.py AlignmentFile ReferenceFile VariantOutputFilename [-q minimal quality score to count base (Default:20)] [-t minimal frequency threshold to call variant (Default:0.03)] [-m minimal number of reads to call variant (Default:0)] [-Q minimal quality score for a base to be considered during pileup (Default: 0)]