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:boolean

Save filtered reads to a file

save_clipstats:boolean

Save clipping stats to a file

Output

name:type
description
pattern

bam

meta:map

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

]

*.clipallowed.bam:file

Clipped reads BAM file

*.{bam}

stats

meta:map

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

]

*.clipstats.txt:file

Clipping statistics text file

*.{clipstats.txt}

rejects_bam

meta:map

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

]

*.cliprejects.bam:file

Filtered reads BAM file

*.{cliprejects.bam}

versions

versions.yml:file

File containing software versions

versions.yml

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
maintainer
Github user bjohnnyd
get in touch
Ask a question on Slack Open an issue on GitHub