Description

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

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

meta (map)

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

vcf (file)

compressed vcf file containing the recalibrated variants.

*.vcf.gz

tbi (file)

Index of recalibrated vcf file.

*vcf.gz.tbi

versions (file)

File containing software versions.

versions.yml
included in
sarek
author
Github user assp8200
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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