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

]

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’ ]

fasta (file)

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

*.{fa,fasta,fna}

meta3 (map)

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

fai (file)

Index of FASTA file. Only needed when fasta is supplied.

*.fai

meta4 (map)

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

fai (file)

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

*.dict

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

metrics (file)

Alignment metrics files generated by picard

*_{metrics}
included in
raredisease variantcatalogue
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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/