Description

Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.

Input

name:type
description
pattern

meta

:map

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

bam

:file

Aligned reads file

*.{bam, cram}

bai

:file

(Optional) Aligned reads file index

*.{bai,crai}

meta2

:map

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

fasta

:file

Genome fasta file

*.{fa,fasta,fna}

meta3

:map

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

fai

:file

Genome fasta file index

*.{fai}

intervallist

:file

Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList.

Output

name:type
description
pattern

metrics

meta

:map

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

*_metrics

:file

Alignment metrics files generated by picard

*_{metrics}

versions_picard

${task.process}

:string

The process the versions were collected from

picard

:string

The tool name

picard CollectWgsMetrics --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 CollectWgsMetrics --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
included in
rarediseasernafusionvariantcatalogue
maintainers
Github user drpatelh
Github user flowuenne
Github user lassefolkersen
Github user ramprasadn
get in touch
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