Description

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

Input

name:type
description
pattern

meta

:map

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

bam

:file

An aligned BAM/CRAM/SAM file

*.{bam,cram,sam}

bai

:file

Optional aligned BAM/CRAM/SAM file index

*.{bai,crai,sai}

bait_intervals

:file

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

*.{interval_list,bed,bed.gz}

target_intervals

:file

An interval file that contains the locations of the targets.

*.{interval_list,bed,bed.gz}

meta2

:map

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

ref

: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

:map

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

ref_fai

:file

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

*.fai

meta4

:map

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

ref_dict

:file

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

*.dict

meta5

:map

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

ref_gzi

:file

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

*.gzi

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 CollectHsMetrics --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 CollectHsMetrics --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 https://github.com/broadinstitute/picard/
included in
methylseqrarediseaseseqinspectorvariantcatalogue
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