modules/gatk4_variantrecalibrator

Build a recalibration model to score variant quality for filtering purposes. It is highly recommended to follow GATK best practices when using this module, the gaussian mixture model requires a large number of samples to be used for the tool to produce optimal results. For example, 30 samples for exome data. For more details see https://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-

gatk4recalibration modelvariantrecalibrator

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

Description

Input

name:type

description

pattern

`meta:map`

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

`vcf:file`

input vcf file containing the variants to be recalibrated

*.vcf.gz

`tbi:file`

tbi file matching with -vcf

*.vcf.gz.tbi

`resource_vcf:file`

all resource vcf files that are used with the corresponding ‘—resource’ label

*.vcf.gz

`resource_tbi:file`

all resource tbi files that are used with the corresponding ‘—resource’ label

*.vcf.gz.tbi

`labels:string`

necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator

`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

`recal`

`meta:file`

Output recal file used by ApplyVQSR

*.recal

`*.recal:file`

Output recal file used by ApplyVQSR

*.recal

`idx`

`meta:file`

Index file for the recal output file

*.idx

`*.idx:file`

Index file for the recal output file

*.idx

`tranches`

`meta:file`

Output tranches file used by ApplyVQSR

*.tranches

`*.tranches:file`

Output tranches file used by ApplyVQSR

*.tranches

`plots`

`meta:file`

Optional output rscript file to aid in visualization of the input data and learned model.

*plots.R

`*plots.R:file`

Optional output rscript file to aid in visualization of the input data and learned model.

*plots.R

`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_variantrecalibrator

Description

Input

`meta:map`

`vcf:file`

`tbi:file`

`resource_vcf:file`

`resource_tbi:file`

`labels:string`

`fasta:file`

`fai:file`

`dict:file`

Output

`recal`

`meta:file`

`*.recal:file`

`idx`

`meta:file`

`*.idx:file`

`tranches`

`meta:file`

`*.tranches:file`

`plots`

`meta:file`

`*plots.R:file`

`versions`

`versions.yml:file`

Tools

gatk4

included in

maintainers

get in touch