NVIDIA Clara Parabricks Pipelines:Joint Calling: TRIOCombineVGCF

Combing 2 or 3 GVCF samples in a fast way


Quick Start

CLI

$ pbrun triocombinegvcf --ref Ref.fa --in-gvcf father.g.vcf \
--in-gvcf mother.g.vcf --in-gvcf child.g.vcf --out-variants combined.g.vcf


Compatible CPU GATK4 Command

$ gatk CombineGVCFs -R Ref.fa -V father.g.vcf -V mother.g.vcf \
-V child.g.vcf -O combined.g.vcf


Options

Option

Description

--ref (required)

The reference file in fasta format.

--in-gvcf (required)

Path to g.vcf or g.vcf.gz file. Option can be used 2 or 3 times.

--out-variants (required)

Path to output merged g.vcf file.