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:false ]

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

ploidy:directory

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

*-calls/

Output

name:type
description
pattern

intervals

meta:map

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

*_genotyped_intervals.vcf.gz:file

Intervals VCF file

*.vcf.gz

s:file

Intervals VCF file

*.vcf.gz

segments

meta:map

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

*_genotyped_segments.vcf.gz:file

Segments VCF file

*.vcf.gz

denoised

meta:map

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

*_denoised.vcf.gz:file

Denoised copy ratio file

*.vcf.gz

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.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/articles/360037593411-PostprocessGermlineCNVCalls 10.1158/1538-7445.AM2017-3590
raredisease
Github user ryanjameskennedy
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