Description

Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list

Input

name:type
description
pattern

meta:map

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

bam:file

List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam

*.{bam}

readlist:file

Optional text file containing reads IDs to include or exclude

filter:string

Picard filter type

includeAligned|excludeAligned|includeReadList|excludeReadList

Output

name:type
description
pattern

bam

meta:map

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

*.bam:file

Filtered BAM file

*.{bam}

versions

versions.yml:file

File containing software versions

versions.yml

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 https://github.com/broadinstitute/picard
rnadnavar
Github user jfy133
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