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 (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 (file)

Output recal file used by ApplyVQSR

*.recal

idx (file)

Index file for the recal output file

*.idx

tranches (file)

Output tranches file used by ApplyVQSR

*.tranches

plots (file)

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

*plots.R

version (file)

File containing software versions

*.versions.yml
included in
sarek
maintainer
Github user asp8200
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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