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
VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.
*.vcf
Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.
*.recal
Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.
.tranches
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.