Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

genoomicsdb (directory)

genomicsDB workspace that contains the samples to create the somatic panel of normals with.

*_genomicsDBworkspace

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 (file)

panel of normal as compressed vcf file

*.vcf.gz

tbi (file)

Tabix index of vcf file

*vcf.gz.tbi

versions (file)

File containing software versions

versions.yml
included in
createpanelrefs
maintainer
Github user GCJMackenzie
get in touch
Ask a question on Slack Open an issue on GitHub

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