Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

input vcf file containing the variants to be recalibrated

*.vcf.gz

tbi{:bash}

:file

tbi file matching with -vcf

*.vcf.gz.tbi

resource_vcf{:bash}

:file

all resource vcf files that are used with the corresponding ‘—resource’ label

*.vcf.gz

resource_tbi{:bash}

:file

all resource tbi files that are used with the corresponding ‘—resource’ label

*.vcf.gz.tbi

labels{:bash}

: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{:bash}

:file

The reference fasta file

*.fasta

fai{:bash}

:file

Index of reference fasta file

fasta.fai

Output

name:type
description
pattern

recal{:bash}

meta{:bash}

:file

Output recal file used by ApplyVQSR

*.recal

*.recal{:bash}

:file

Output recal file used by ApplyVQSR

*.recal

idx{:bash}

meta{:bash}

:file

Output recal file used by ApplyVQSR

*.recal

*.idx{:bash}

:file

Index file for the recal output file

*.idx

tranches{:bash}

meta{:bash}

:file

Output recal file used by ApplyVQSR

*.recal

*.tranches{:bash}

:file

Output tranches file used by ApplyVQSR

*.tranches

plots{:bash}

meta{:bash}

:file

Output recal file used by ApplyVQSR

*.recal

*plots.R{:bash}

:file

Optional output rscript file to aid in visualization of the input data and learned model.

*plots.R

versions{:bash}

versions.yml{:bash}

: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
included in
sarek
maintainer
Github user asp8200
get in touch
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