Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

genomicsdb{:bash}

:file

GenomicsDB database

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

meta4{:bash}

:map

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

dict{:bash}

:file

GATK sequence dictionary

*.dict

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

A Groovy map containing sample information

*.vcf.gz{:bash}

:file

panel of normal as compressed vcf file

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

A Groovy map containing sample information

*.tbi{:bash}

:file

Tabix index of vcf file

*vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

: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
included in
createpanelrefs
maintainer
Github user GCJMackenzie
get in touch
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