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

versions.yml: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
methylseqrarediseasevariantcatalogue
maintainers
Github user projectoriented
Github user matthdsm
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