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

]

bam (file)

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

*.{bam}

filter (string)

Picard filter type

includeAligned|excludeAligned|includeReadList|excludeReadList

readlist (file)

Optional text file containing reads IDs to include or exclude

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

Filtered BAM file

*.{bam}

versions (file)

File containing software versions

versions.yml
included in
rnadnavar
author
Github user jfy133
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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 https://github.com/broadinstitute/picard