Description

Clips read alignments where they match BED file defined regions

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

bed (file)

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

*.{bed}

save_cliprejects (value)

Save filtered reads to a file

save_clipstats (value)

Save clipping stats to a file

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

bam (file)

Clipped reads BAM file

*.{bam}

stats (file)

Clipping statistics text file

*.{clipstats.txt}

rejects_bam (file)

Filtered reads BAM file

*.{cliprejects.bam}
author
Github user bjohnnyd
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

samtools
MIT

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.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352