At the moment, if a SNP has a valid map but its alleles are not in the reference sequence it will be discarded; this is a valid alignment, however, SNP can be saved by setting REF as the reference sequences and ALT as SNP alleles (ALT should be a LIST)
At the moment, if a SNP has a valid map but its alleles are not in the reference sequence it will be discarded; this is a valid alignment, however, SNP can be saved by setting REF as the reference sequences and ALT as SNP alleles (ALT should be a LIST)