modules/sentieon_varcal

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

sentieonvarcalvariant recalibration

https://github.com/nf-core/modules/[...]/modules/nf-core/sentieon/varcal

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 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

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

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.

sentieon.com