Description

Denoises read counts to produce denoised copy ratios

Input

name:type
description
pattern

meta:map

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

counts:file

Read counts in hdf5 or tsv format.

*.{hdf5,tsv}

meta2:map

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

pon:file

Panel of normals file hdf5 or tsv format.

*.{hdf5}

Output

name:type
description
pattern

standardized

meta:map

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

*_standardizedCR.tsv:file

Standardized copy ratios file.

*.{tsv}

denoised

meta:map

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

*_denoisedCR.tsv:file

Denoised copy ratios file

*.{tsv}

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/categories/360002369672s https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590
included in
raredisease
maintainer
Github user ramprasadn
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