Description

Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.

Input

name:type
description
pattern

meta{:bash}

:map

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

tsv{:bash}

:file

One or more count TSV files created with gatk/collectreadcounts

*.tsv

intervals{:bash}

:file

Optional - A bed file containing the intervals to include in the process

*.bed

ploidy{:bash}

:directory

Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode

*-calls

model{:bash}

:directory

Optional - directory containing the model produced by germlinecnvcaller cohort mode

*-cnv-model/*-model

Output

name:type
description
pattern

cohortcalls{:bash}

meta{:bash}

:map

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

*-cnv-model/*-calls{:bash}

:directory

Tar gzipped directory containing calls produced by germlinecnvcaller case mode

*-cnv-model/*-calls

cohortmodel{:bash}

meta{:bash}

:map

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

*-cnv-model/*-model{:bash}

:directory

Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode

*-cnv-model/*-model

casecalls{:bash}

meta{:bash}

:map

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

*-cnv-calls/*-calls{:bash}

:directory

Tar gzipped directory containing calls produced by germlinecnvcaller case mode

*-cnv-calls/*-calls

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
createpanelrefsraredisease
maintainers
Github user ryanjameskennedy
Github user ViktorHy
get in touch
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