Description

Collect multiple metrics from a BAM file

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

SAM/BAM/CRAM file

*.{sam,bam,cram}

bai (file)

Optional SAM/BAM/CRAM file index

*.{sai,bai,crai}

meta2 (map)

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

fasta (file)

Genome fasta file

meta3 (map)

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

fai (file)

Index of FASTA file. Only needed when fasta is supplied.

*.fai

Output

Name (Type)
Description
Pattern

meta (map)

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

]

metrics (file)

Alignment metrics files generated by picard

*_{metrics}

pdf (file)

PDF plots of metrics

*.{pdf}

versions (file)

File containing software versions

versions.yml
included in
atacseq callingcards chipseq raredisease ssds viralrecon
maintainer
Github user drpatelh
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