Description

Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel.

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}

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

pon (file)

Panel-of-normals file.

*.{hdf5}
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