Description

Clips read alignments where they match BED file defined regions

Input

Name
Description
Pattern

0 ()

1 ()

bed (file)

BED file of regions to be removed (e.g. amplicon primers)

*.{bed}

save_cliprejects (boolean)

Save filtered reads to a file

save_clipstats (boolean)

Save clipping stats to a file

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

Tools

samtools Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT
Authors