modules/sentieon_applyvarcal

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

sentieonapplyvarcalvarcalVQSR

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

Description

Input

name:type

description

pattern

`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

`meta2`
`:map`

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

`fasta`
`:file`

The reference fasta file

*.fasta

`meta3`
`:map`

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

`fai`
`:file`

Index of reference fasta file

*.fasta.fai

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

compressed vcf file containing the recalibrated variants.

*.vcf.gz

`tbi`

`meta`
`:map`

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

`*.tbi`
`:file`

Index of recalibrated vcf file.

*vcf.gz.tbi

`versions_sentieon`

`${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

Topics

name:type

description

pattern

`versions`

`${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

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

modules/sentieon_applyvarcal

Description

Input

`meta`
`:map`

`vcf`
`:file`

`vcf_tbi`
`:file`

`recal`
`:file`

`recal_index`
`:file`

`tranches`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`versions_sentieon`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

Tools

sentieon

included in

maintainer

get in touch

modules/sentieon_applyvarcal

Description

Input

meta:map

vcf:file

vcf_tbi:file

recal:file

recal_index:file

tranches:file

meta2:map

fasta:file

meta3:map

fai:file

Output

vcf

meta:map

*.vcf.gz:file

tbi

meta:map

*.tbi:file

versions_sentieon

${task.process}:string

sentieon:string

sentieon driver --version | sed "s/.*-//g":string

Topics

versions

${task.process}:string

sentieon:string

sentieon driver --version | sed "s/.*-//g":string

Tools

sentieon

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`vcf_tbi`
`:file`

`recal`
`:file`

`recal_index`
`:file`

`tranches`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`versions_sentieon`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

`versions`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`