Usage: biscuit qc_coverage <ref.fa> <cpgs.bed.gz> <in.bam>
Options:
-P STR Prefix for output file names
-B STR Bottom 10 percent GC content windows BED file
-T STR Top 10 percent GC content windows BED file
-s INT Step size of windows [100000]
-@ INT Number of threads [3]
Filter options:
-b INT Minimum base quality [20]
-a INT Minimum alignment score (from AS-tag) [40]
-t INT Max cytosine retention in a read [999999]
-l INT Minimum read length [10]
-u NO filtering of duplicate reads
-p NO filtering of improper pair
-n INT Maximum NM tag [999999]
-h Print usage