Optionally provide a strand_file in BED format, indicating the regions where the reverse strand should be used to define mutation type. Sites not in the BED file's regions will use the forward strand.
This could be useful to polarize context according to direction of replication or transcription.
If the argument is not used, the usual collapase-by-reverse-complement approach is used.
Optionally provide a
strand_filein BED format, indicating the regions where the reverse strand should be used to define mutation type. Sites not in the BED file's regions will use the forward strand.This could be useful to polarize context according to direction of replication or transcription.
If the argument is not used, the usual collapase-by-reverse-complement approach is used.