modules/sentieon_applyvarcal

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

sentieonapplyvarcalvarcalVQSR

https://github.com/nf-core/modules/[...]/modules/nf-core/sentieon/applyvarcal

Description

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

`vcf`

`meta:map`

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

`*.vcf.gz:file`

compressed vcf file containing the recalibrated variants.

*.vcf.gz

`tbi`

`meta:map`

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

`*.tbi:file`

Index of recalibrated vcf file.

*vcf.gz.tbi

`versions`

`versions.yml: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