Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

Aligned reads file

*.{bam, cram}

bai{:bash}

:file

(Optional) Aligned reads file index

*.{bai,crai}

meta2{:bash}

:map

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

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta,fna}

meta3{:bash}

:map

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

fai{:bash}

:file

Genome fasta file index

*.{fai}

intervallist{:bash}

: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{:bash}

meta{:bash}

:map

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

*_metrics{:bash}

:file

Alignment metrics files generated by picard

*_{metrics}

versions{:bash}

versions.yml{:bash}

: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
included in
rarediseasernafusionvariantcatalogue
maintainers
Github user drpatelh
Github user flowuenne
Github user lassefolkersen
Github user ramprasadn
get in touch
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