Description

Prepares bins for coverage collection.

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta2{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

meta3{:bash}

:map

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

dict{:bash}

:file

GATK sequence dictionary

*.dict

meta4{:bash}

:map

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

intervals{:bash}

:file

Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional)

*.{bed,interval_list}

meta5{:bash}

:map

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

exclude_intervals{:bash}

:file

Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional)

*.{bed,interval_list}

Output

name:type
description
pattern

interval_list{:bash}

meta{:bash}

:map

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

*.interval_list{:bash}

:file

Processed interval list file

*.{bed,interval_list}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590
included in
createpanelrefs
maintainers
Github user ryanjameskennedy
Github user ViktorHy
Github user ramprasadn
get in touch
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