Closed MatthieuBeukers closed 5 years ago
Require a reference sequence, and check to make sure the reference sequences in the BAM/CRAM/VCF/etc. contain the same reference sequences. Otherwise, complain.
Fixed this with a check using the genome reference
Depending on the SAM/BAM/CRAM file, chromosomes can be preceded by 'chr' (e.g. chr21, chrX, etc)