Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

f1r2{:bash}

:list

list of f1r2 files to be used as input.

*.f1r2.tar.gz

Output

name:type
description
pattern

artifactprior{:bash}

meta{:bash}

:file

file containing artifact-priors to be used by filtermutectcalls

*.tar.gz

*.tar.gz{:bash}

:file

file containing artifact-priors to be used by filtermutectcalls

*.tar.gz

versions{:bash}

versions.yml{:bash}

: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 10.1158/1538-7445.AM2017-3590
included in
rnadnavarsarek
maintainer
Github user GCJMackenzie
get in touch
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