Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

tsv (file)

One or more count TSV files created with gatk/collectreadcounts

*.tsv

intervals (file)

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

*.bed

model (directory)

Optional - directory containing the model produced by germlinecnvcaller cohort mode

*-cnv-model/*-model

ploidy (directory)

Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode

*-calls

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

cohortcalls (directory)

Tar gzipped directory containing calls produced by germlinecnvcaller case mode

*-cnv-model/*-calls

cohortmodel (directory)

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

*-cnv-model/*-model

casecalls (directory)

Tar gzipped directory containing calls produced by germlinecnvcaller case mode

*-cnv-calls/*-calls
included in
createpanelrefs raredisease
authors
Github user ryanjameskennedy Github user ViktorHy
get in touch
Ask a question on Slack Open an issue on GitHub

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