Description

Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios

Input

Name (Type)
Description
Pattern

meta (map)

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

]

ploidy (directory)

Optional - A folder containing the ploidy model.
When a model is supplied to tool will run in CASE mode.

*-calls/

calls (directory)

A folder containing the calls from the input files

*-cnv-calls/*-calls

model (directory)

A folder containing the model from the input files.
This will only be created in COHORT mode (when no model is supplied to the process).

*-cnv-model/*-model

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

denoised (file)

Denoised copy ratio file

*.vcf.gz

segments (file)

Segments VCF file

*.vcf.gz

intervals (file)

Intervals VCF file

*.vcf.gz
included in
raredisease
author
Github user ryanjameskennedy
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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/articles/360037593411-PostprocessGermlineCNVCalls 10.1158/1538-7445.AM2017-3590