Description

trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file

*.bam

trim_left{:bash}

:integer

Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.

trim_right{:bash}

:integer

Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

Trimmed but unsorted BAM file

*.bam

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

bamutil
GPL v3

Programs that perform operations on SAM/BAM files, all built into a single executable, bam.

genome.sph.umich.edu/wiki/BamUtil genome.sph.umich.edu/wiki/BamUtil:_trimBam https://github.com/statgen/bamUtil 10.1101/gr.176552.114
maintainer
Github user jfy133
get in touch
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