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{:bash}

:map

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

vcf{:bash}

:file

VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.

*.vcf

vcf_tbi{:bash}

:file

tabix index for the input vcf file.

*.vcf.tbi

recal{:bash}

:file

Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.

*.recal

recal_index{:bash}

:file

Index file for the recalibration file.

.recal.idx

tranches{:bash}

:file

Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.

.tranches

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

compressed vcf file containing the recalibrated variants.

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.tbi{:bash}

:file

Index of recalibrated vcf file.

*vcf.gz.tbi

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 assp8200
get in touch
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