Description

Collects hybrid-selection (HS) metrics for a SAM or BAM file.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

An aligned BAM/CRAM/SAM file

*.{bam,cram,sam}

bai{:bash}

:file

Optional aligned BAM/CRAM/SAM file index

*.{bai,crai,sai}

bait_intervals{:bash}

:file

An interval file that contains the locations of the baits used.

*.{interval_list,bed,bed.gz}

target_intervals{:bash}

:file

An interval file that contains the locations of the targets.

*.{interval_list,bed,bed.gz}

meta2{:bash}

:map

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

ref{:bash}

:file

A reference file to calculate dropout metrics measuring reduced representation of reads. Optional input.

*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}

meta3{:bash}

:map

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

ref_fai{:bash}

:file

Index of reference file. Only needed when reference is supplied.

*.fai

meta4{:bash}

:map

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

ref_dict{:bash}

:file

Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.

*.dict

meta5{:bash}

:map

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

ref_gzi{:bash}

:file

Index of reference file. Only needed when gzipped reference is supplied.

*.gzi

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 https://github.com/broadinstitute/picard/
included in
methylseqrarediseaseseqinspectorvariantcatalogue
maintainers
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Github user matthdsm
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