modules/gatk4_createreadcountpanelofnormals

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

createreadcountpanelofnormalsgatk4panelofnormals

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/createreadcountpanelofnormals

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

`pon`

`meta:map`

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

`*.hdf5:file`

Panel-of-normals file.

*.{hdf5}

`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

modules/gatk4_createreadcountpanelofnormals

Description

Input

meta:map

counts:file

Output

pon

meta:map

*.hdf5:file

versions

versions.yml:file

Tools

gatk4 Apache-2.0

`meta:map`

`counts:file`

`pon`

`meta:map`

`*.hdf5:file`

`versions`

`versions.yml:file`

gatk4
Apache-2.0