modules/gatk4_createsomaticpanelofnormals

Create a panel of normals constraining germline and artifactual sites for use with mutect2.

createsomaticpanelofnormalsgatk4panelofnormals

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

Description

Create a panel of normals constraining germline and artifactual sites for use with mutect2.

Input

name:type

description

pattern

`meta:map`

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

`genomicsdb:file`

GenomicsDB database

`meta2:map`

Groovy Map containing reference information e.g. [ id:‘test’]

`fasta:file`

The reference fasta file

*.fasta

`meta3:map`

Groovy Map containing reference information e.g. [ id:‘test’]

`fai:file`

Index of reference fasta file

*.fasta.fai

`meta4:map`

Groovy Map containing reference information e.g. [ id:‘test’]

`dict:file`

GATK sequence dictionary

*.dict

Output

name:type

description

pattern

`vcf`

`meta:file`

panel of normal as compressed vcf file

*.vcf.gz

`*.vcf.gz:file`

panel of normal as compressed vcf file

*.vcf.gz

`tbi`

`meta:file`

Tabix index of vcf file

*vcf.gz.tbi

`*.tbi:file`

Tabix index of vcf file

*vcf.gz.tbi

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

gatk4

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 10.1158/1538-7445.AM2017-3590