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

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

Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR). VarCal builds a recalibration model for scoring variant quality. https://support.sentieon.com/manual/usages/general/#varcal-algorithm

sentieon varcal variant recalibration

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @asp8200

Maintainers: @asp8200

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

include { SENTIEON_VARCAL } from 'nf-core/sentieon/varcal'

MIT License

Process

`Name`	`SENTIEON_VARCAL`

Input 6 channels

#1 tuple

`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 Sentieon's VarCal. Specified to directly match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm

`fasta` file	The reference fasta file `*.fasta`

`fai` file	Index of reference fasta file `fasta.fai`

Output 5 channels

#1 idx tuple

`meta` file	Output recal file used by ApplyVQSR `*.recal`
`*.idx` file	Index file for the recal output file `*.idx`

#2 plots tuple

`meta` file	Output recal file used by ApplyVQSR `*.recal`
`*plots.R` file	Optional output rscript file to aid in visualization of the input data and learned model. `*plots.R`

#3 recal tuple

`meta` file	Output recal file used by ApplyVQSR `*.recal`
`*.recal` file	Output recal file used by ApplyVQSR `*.recal`

#4 tranches tuple

`meta` file	Output recal file used by ApplyVQSR `*.recal`
`*.tranches` file	Output tranches file used by ApplyVQSR `*.tranches`

#5 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 15:44:14 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Fvarcal/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sentieon/varcal/blobs/sha256:db8d908a4514f3ab2a4f1cb374b1652ecfda28133857e31c3401eb4aa6da6360