Nextflow Registry | nf-core/gatk4/filtermutectcalls@0.0.0-6c4ed3a

nf-core/gatk4/filtermutectcalls @ 0.0.0-6c4ed3a

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

filtermutectcalls filter gatk4 mutect2 vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @GCJMackenzie @maxulysse @ramprasadn

Maintainers: @GCJMackenzie @maxulysse @ramprasadn

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

Add the following snippet to your workflow script to include this module.

include { GATK4_FILTERMUTECTCALLS } from 'nf-core/gatk4/filtermutectcalls'

MIT License

Process

`Name`	`GATK4_FILTERMUTECTCALLS`

Input 4 channels

#1 tuple

`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.

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	The reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fai` file	Index of reference fasta file `*.fasta.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`dict` file	GATK sequence dictionary `*.dict`

Output 4 channels

#1 tbi tuple

`meta` file	file containing filtered mutect2 calls. `*.vcf.gz`
`*.vcf.gz.tbi` file	tbi file that pairs with vcf. `*.vcf.gz.tbi`

#2 vcf tuple

`meta` file	file containing filtered mutect2 calls. `*.vcf.gz`
`*.vcf.gz` file	file containing filtered mutect2 calls. `*.vcf.gz`

#3 stats tuple

`meta` file	file containing filtered mutect2 calls. `*.vcf.gz`
`*.filteringStats.tsv` file	file containing statistics of the filtermutectcalls run. `*.filteringStats.tsv`

#4 versions_gatk4 tuple

`${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

Tool	Description	Homepage
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.	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-6c4ed3a