Additional options

ImReP offers additional options. For example, one can select the genome release the reads were mapped to using -hg38 option. By default, we assume reads were mapped onto hg19 release

python imrep.py --hg38 --bam example/toyExample.bam example/toyExample.cdr3

In case the chromosome names are in UCSC format (i.e. are composed of string chr and the chromosome number). For example, chr1. In this case, you need to use --chrFormat2 option