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:false ]

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

ploidy:directory

Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode

*-calls

model:directory

Optional - directory containing the model produced by germlinecnvcaller cohort mode

*-cnv-model/*-model

Output

name:type
description
pattern

cohortcalls

meta:map

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

*-cnv-model/*-calls:directory

Tar gzipped directory containing calls produced by germlinecnvcaller case mode

*-cnv-model/*-calls

cohortmodel

meta:map

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

*-cnv-model/*-model:directory

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

*-cnv-model/*-model

casecalls

meta:map

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

*-cnv-calls/*-calls:directory

Tar gzipped directory containing calls produced by germlinecnvcaller case mode

*-cnv-calls/*-calls

versions

versions.yml: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.