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 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`

`meta:file`

file containing filtered mutect2 calls.

*.vcf.gz

`*.vcf.gz:file`

file containing filtered mutect2 calls.

*.vcf.gz

`tbi`

`meta:file`

tbi file that pairs with vcf.

*.vcf.gz.tbi

`*.vcf.gz.tbi:file`

tbi file that pairs with vcf.

*.vcf.gz.tbi

`stats`

`meta:file`

file containing statistics of the filtermutectcalls run.

*.filteringStats.tsv

`*.filteringStats.tsv:file`

file containing statistics of the filtermutectcalls run.

*.filteringStats.tsv

`versions`

`versions.yml: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

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`

`meta3:map`

`fai:file`

`meta4:map`

`dict:file`

Output

`vcf`

`meta:file`

`*.vcf.gz:file`

`tbi`

`meta:file`

`*.vcf.gz.tbi:file`

`stats`

`meta:file`

`*.filteringStats.tsv:file`

`versions`

`versions.yml:file`

Tools

gatk4

included in

maintainers

get in touch