modules/gatk4_filtermutectcalls

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

filtermutectcallsfiltergatk4mutect2vcf

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/filtermutectcalls

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 the input vcf file (Mutect2 or MergeMutectStats output). Passed to FilterMutectCalls via –stats. If not provided, GATK looks for .stats next to the input vcf.

*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

`fai`
`:file`

Index of reference fasta file

*.fasta.fai

`dict`
`:file`

GATK sequence dictionary

*.dict

Output

name:type

description

pattern

`vcf`

`meta`
`:file`

file containing filtered mutect2 calls.

*.vcf.gz

`*.vcf.gz`
`:file`

file containing filtered mutect2 calls.

*.vcf.gz

`tbi`

`meta`
`:file`

file containing filtered mutect2 calls.

*.vcf.gz

`*.vcf.gz.tbi`
`:file`

tbi file that pairs with vcf.

*.vcf.gz.tbi

`stats`

`meta`
`:file`

file containing filtered mutect2 calls.

*.vcf.gz

`*.filteringStats.tsv`
`:file`

file containing statistics of the filtermutectcalls run.

*.filteringStats.tsv

`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

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

modules/gatk4_filtermutectcalls

Description

Input

`meta`
`:map`

`vcf`
`:file`

`vcf_tbi`
`:file`

`stats`
`:file`

`orientationbias`
`:file`

`segmentation`
`:file`

`table`
`:file`

`estimate`
`:float`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`dict`
`:file`

Output

`vcf`

`meta`
`:file`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:file`

`*.vcf.gz.tbi`
`:file`

`stats`

`meta`
`:file`

`*.filteringStats.tsv`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4

maintainers

get in touch

modules/gatk4_filtermutectcalls

Description

Input

meta :map

vcf :file

vcf_tbi :file

stats :file

orientationbias :file

segmentation :file

table :file

estimate :float

meta2 :map

fasta :file

fai :file

dict :file

Output

vcf

meta :file

*.vcf.gz :file

tbi

meta :file

*.vcf.gz.tbi :file

stats

meta :file

*.filteringStats.tsv :file

versions_gatk4

${task.process} :string

gatk4 :string

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

Topics

versions

${task.process} :string

gatk4 :string

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

Tools

gatk4

maintainers

get in touch

`meta`
`:map`

`vcf`
`:file`

`vcf_tbi`
`:file`

`stats`
`:file`

`orientationbias`
`:file`

`segmentation`
`:file`

`table`
`:file`

`estimate`
`:float`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`dict`
`:file`

`vcf`

`meta`
`:file`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:file`

`*.vcf.gz.tbi`
`:file`

`stats`

`meta`
`:file`

`*.filteringStats.tsv`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`