Description

Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

compressed vcf file of mutect2calls

*.vcf.gz

vcf_tbi{:bash}

:file

Tabix index of vcf file

*vcf.gz.tbi

stats{:bash}

:file

Stats file that pairs with output vcf file

*vcf.gz.stats

orientationbias{:bash}

:file

files containing artifact priors for input vcf. Optional input.

*.artifact-prior.tar.gz

segmentation{:bash}

:file

tables containing segmentation information for input vcf. Optional input.

*.segmentation.table

table{:bash}

:file

table(s) containing contamination data for input vcf. Optional input, takes priority over estimate.

*.contamination.table

estimate{:bash}

:float

estimation of contamination value as a double. Optional input, will only be used if table is not specified.

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

meta4{:bash}

:map

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

dict{:bash}

:file

GATK sequence dictionary

*.dict

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:file

file containing filtered mutect2 calls.

*.vcf.gz

*.vcf.gz{:bash}

:file

file containing filtered mutect2 calls.

*.vcf.gz

tbi{:bash}

meta{:bash}

:file

file containing filtered mutect2 calls.

*.vcf.gz

*.vcf.gz.tbi{:bash}

:file

tbi file that pairs with vcf.

*.vcf.gz.tbi

stats{:bash}

meta{:bash}

:file

file containing filtered mutect2 calls.

*.vcf.gz

*.filteringStats.tsv{:bash}

:file

file containing statistics of the filtermutectcalls run.

*.filteringStats.tsv

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
rarediseasernadnavarsarekvariantcatalogue
maintainers
Github user GCJMackenzie
Github user maxulysse
Github user ramprasadn
get in touch
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