There is a small issue with this script. It is assuming that chromosome names always start with 'chr'.(line 31). However in some situations this is not the case. For example I'm working with pig data and the genome files I downloaded and used for the alignment do not have 'chr'.
There is a small issue with this script. It is assuming that chromosome names always start with 'chr'.(line 31). However in some situations this is not the case. For example I'm working with pig data and the genome files I downloaded and used for the alignment do not have 'chr'.