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 (map)

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

]

bam (file)

BAM file

*.bam

trim_left (integer)

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

trim_right (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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

Trimmed but unsorted BAM file

*.bam
maintainer
Github user jfy133
get in touch
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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