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:false ]

bam

:file

BAM file

*.{bam}

Output

name:type
description
pattern

bam

meta

:map

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

*.bam

:file

Cleaned BAM file

*.{bam}

versions_picard

${task.process}

:string

The process the versions were collected from

picard

:string

The tool name

picard CleanSam --version 2>&1 | sed -n 's/.*Version://p'

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

picard

:string

The tool name

picard CleanSam --version 2>&1 | sed -n 's/.*Version://p'

:string

The command used to generate the version of the tool

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
maintainers
Github user sateeshperi
Github user mjcipriano
Github user hseabolt
get in touch
Ask a question on Slack Open an issue on GitHub