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

]

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

meta (map)

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

]

metrics (file)

Alignment metrics files generated by picard

*_{metrics}

versions (file)

File containing software versions

versions.yml
included in
raredisease rnafusion variantcatalogue
maintainers
Github user drpatelh
Github user flowuenne
Github user lassefolkersen
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub

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