Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

vcf (file)

compressed vcf file of mutect2calls

*.vcf.gz

vcf_tbi (file)

Tabix index of vcf file

*vcf.gz.tbi

stats (file)

Stats file that pairs with output vcf file

*vcf.gz.stats

orientationbias (file)

files containing artifact priors for input vcf. Optional input.

*.artifact-prior.tar.gz

segmentation (file)

tables containing segmentation information for input vcf. Optional input.

*.segmentation.table

table (file)

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

*.contamination.table

estimate (float)

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

meta2 (map)

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

fasta (file)

The reference fasta file

*.fasta

meta3 (map)

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

fai (file)

Index of reference fasta file

*.fasta.fai

meta4 (map)

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

dict (file)

GATK sequence dictionary

*.dict

Output

Name (Type)
Description
Pattern

vcf (file)

file containing filtered mutect2 calls.

*.vcf.gz

tbi (file)

tbi file that pairs with vcf.

*.vcf.gz.tbi

stats (file)

file containing statistics of the filtermutectcalls run.

*.filteringStats.tsv

versions (file)

File containing software versions

versions.yml
included in
raredisease rnadnavar sarek variantcatalogue
maintainers
Github user GCJMackenzie
Github user maxulysse
Github user ramprasadn
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