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
Description
Pattern

0 ()

1 ()

2 ()

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
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

sentieon Documentation

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.

Authors