Description

Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads

Input

Name (Type)
Description
Pattern

meta (map)

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

]

sam (file)

BAM file

*.{bam}

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

sam (file)

Cleaned BAM file

*.{bam}
authors
Github user sateeshperi Github user mjcipriano Github user hseabolt
get in touch
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Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

broadinstitute.github.io/picard gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard- https://github.com/broadinstitute/picard