Nextflow Registry | nf-core/sentieon/applyvarcal@0.0.0-6c4ed3a

nf-core/sentieon/applyvarcal @ 0.0.0-6c4ed3a

Apply a score cutoff to filter variants based on a recalibration table. Sentieon's Aplyvarcal 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 previous step VarCal and a target sensitivity value. https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm

sentieon applyvarcal varcal VQSR

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @assp8200

Maintainers: @assp8200

Summary

Get started

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

include { SENTIEON_APPLYVARCAL } from 'nf-core/sentieon/applyvarcal'

License

MIT License

Process

`Name`	`SENTIEON_APPLYVARCAL`

Input 3 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`

#2 tuple

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

#3 tuple

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

Output 3 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`*.tbi` file	Index of recalibrated vcf file. `*vcf.gz.tbi`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`*.vcf.gz` file	compressed vcf file containing the recalibrated variants. `*.vcf.gz`

#3 versions_sentieon tuple

`${task.process}` string	The process the versions were collected from
`sentieon` string	The tool name
`sentieon driver --version \| sed "s/.*-//g"` string	The command used to generate the version of the tool

Tool	Description	Homepage
sentieon	Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.	https://www.sentieon.com/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:43:51 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Fapplyvarcal/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sentieon/applyvarcal/blobs/sha256:3434bec9deb025585c9beac319dc1deeacc3e0b8409ef055567a280a53a55652
Size	3.6 KB
Checksum	sha256:3434bec9deb025585c9beac319dc1deeacc3e0b8409ef055567a280a53a55652
Downloads	2