modules/gatk4_applyvqsr
Apply a score cutoff to filter variants based on a recalibration table. AplyVQSR 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 first step by VariantRecalibrator and a target sensitivity value.
Description
Apply a score cutoff to filter variants based on a recalibration table. AplyVQSR 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 first step by VariantRecalibrator and a target sensitivity value.
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
gatk4 Apache-2.0
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.