Alignment utilities

Alignment utilities operate on SAM, BAM, or CRAM files produced by the mapping stages.

Commands

Command	Purpose
samclip	Filter clipped reads from SAM alignments.
cnv	Estimate contig or feature copy numbers from aligned BAM or CRAM depth.

Notes

The samclip command is boundary-aware. A read is filtered when either terminal clip exceeds the threshold, except when the clipped end reaches the contig boundary. Fraction mode uses the total terminal clipping divided by the original query length, including hard clips.