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`

Output recal file used by ApplyVQSR

*.recal

`*.idx`
`:file`

Index file for the recal output file

*.idx

`tranches`

`meta`
`:file`

Output recal file used by ApplyVQSR

*.recal

`*.tranches`
`:file`

Output tranches file used by ApplyVQSR

*.tranches

`plots`

`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

`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_varcal

Description

Input

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`resource_vcf`
`:file`

`resource_tbi`
`:file`

`labels`
`:string`

`fasta`
`:file`

`fai`
`:file`

Output

`recal`

`meta`
`:file`

`*.recal`
`:file`

`idx`

`meta`
`:file`

`*.idx`
`:file`

`tranches`

`meta`
`:file`

`*.tranches`
`:file`

`plots`

`meta`
`:file`

`*plots.R`
`: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_varcal

Description

Input

meta:map

vcf:file

tbi:file

resource_vcf:file

resource_tbi:file

labels:string

fasta:file

fai:file

Output

recal

meta:file

*.recal:file

idx

meta:file

*.idx:file

tranches

meta:file

*.tranches:file

plots

meta:file

*plots.R: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`

`tbi`
`:file`

`resource_vcf`
`:file`

`resource_tbi`
`:file`

`labels`
`:string`

`fasta`
`:file`

`fai`
`:file`

`recal`

`meta`
`:file`

`*.recal`
`:file`

`idx`

`meta`
`:file`

`*.idx`
`:file`

`tranches`

`meta`
`:file`

`*.tranches`
`:file`

`plots`

`meta`
`:file`

`*plots.R`
`: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`