Description

Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts

Input

name:type
description
pattern

meta

:map

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

f1r2

:list

list of f1r2 files to be used as input.

*.f1r2.tar.gz

Output

name:type
description
pattern

artifactprior

meta

:file

file containing artifact-priors to be used by filtermutectcalls

*.tar.gz

*.tar.gz

:file

file containing artifact-priors to be used by filtermutectcalls

*.tar.gz

versions_gatk4

${task.process}

:string

The name of the process

gatk4

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

gatk4

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'

:eval

The expression to obtain the version of the tool

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.