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nf-core/gatk4/applyvqsr @ 0.0.0-0c7146d

Apply a score cutoff to filter variants based on a recalibration table. AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the first step by VariantRecalibrator and a target sensitivity value.

gatk4 variant quality score recalibration vcf vqsr
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @GCJMackenzie
Maintainers: @GCJMackenzie

Summary

Apply a score cutoff to filter variants based on a recalibration table. AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the first step by VariantRecalibrator and a target sensitivity value.

Get started

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

include { GATK4_APPLYVQSR } from 'nf-core/gatk4/applyvqsr'

License

MIT License

Process
Name GATK4_APPLYVQSR
Input 4 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test']
vcf file

VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.

 *.vcf
vcf_tbi file

tabix index for the input vcf file.

 *.vcf.tbi
recal file

Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.

 *.recal
recal_index file

Index file for the recalibration file.

 .recal.idx
tranches file

Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.

 .tranches
fasta file

The reference fasta file

 *.fasta
fai file

Index of reference fasta file

 *.fasta.fai
dict file

GATK sequence dictionary

 *.dict
Output 3 channels
#1 tbi tuple
meta file

compressed vcf file containing the recalibrated variants.

 *.vcf.gz
*.tbi file

Index of recalibrated vcf file.

 *vcf.gz.tbi
#2 vcf tuple
meta file

compressed vcf file containing the recalibrated variants.

 *.vcf.gz
*.vcf.gz file

compressed vcf file containing the recalibrated variants.

 *.vcf.gz
#3 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 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:41:00 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fapplyvqsr/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/applyvqsr/blobs/sha256:04ef43ac6fbcc45f5784e08c4d865c1d2ada973b5423a8d861c0d5ee88b028f2
Size 3.6 KB
Checksum sha256:04ef43ac6fbcc45f5784e08c4d865c1d2ada973b5423a8d861c0d5ee88b028f2
Downloads 1
Version Date Status Downloads Size Diff
0.0.0-0c7146d 08 Apr 2026 18:41:00 (UTC) 1 3.6 KB