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 ]

meta2 (map)

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

counts (file)

Read counts in hdf5 or tsv format.

*.{hdf5,tsv}

pon (file)

Panel of normals file hdf5 or tsv format.

*.{hdf5}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

standardized (file)

Standardized copy ratios file.

*.{tsv}

denoised (file)

Denoised copy ratios file

*.{tsv}
author
Github user ramprasadn
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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/categories/360002369672s https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590