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

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

fasta{:bash}

:file

The reference fasta file

*.fasta

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

dict{:bash}

:file

GATK sequence dictionary

*.dict

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:file

compressed vcf file containing the recalibrated variants.

*.vcf.gz

*.vcf.gz{:bash}

:file

compressed vcf file containing the recalibrated variants.

*.vcf.gz

tbi{:bash}

meta{:bash}

:file

compressed vcf file containing the recalibrated variants.

*.vcf.gz

*.tbi{:bash}

:file

Index of recalibrated vcf file.

*vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions.

versions.yml

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.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590
included in
sarektbanalyzer
maintainer
Github user GCJMackenzie
get in touch
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