Description

Locate and tag duplicate reads in a BAM file

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file

*.{bam,cram,sam}

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta (file)

Reference genome fasta file

*.{fasta,fa}

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fai (file)

Reference genome fasta index

*.{fai}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file with duplicate reads marked/removed

*.{bam}

bai (file)

An optional BAM index file. If desired, —CREATE_INDEX must be passed as a flag

*.{bai}

metrics (file)

Duplicate metrics file generated by picard

*.{metrics.txt}

versions (file)

File containing software versions

versions.yml
included in
atacseq chipseq circdna cutandrun methylseq pathogensurveillance raredisease rnadnavar rnafusion rnaseq ssds viralrecon
authors
Github user drpatelh Github user projectoriented Github user ramprasadn
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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