genotypegvcf

This tool converts variant calls in g.vcf format to vcf format.

Quick Start

$ pbrun genotypegvcf --ref Ref.fa --in-gvcf input.g.vcf --out-vcf output.vcf

Compatible CPU GATK4 Command

$ gatk GenotypeGVCFs -R Ref.fa -V input.g.vcf -O output.vcf

Options

Option

Description

--ref (required)

Input Reference file in fasta format.

--in-gvcf

Input g.vcf file that will be converted to vcf. Required if --in-selectvariants-dir is not specified.

--in-selectvariants-dir

Path to the output directory of selectvariants. Required if --in-gvcf is not specified.

--out-vcf (required)

Output vcf file.

--num-threads

Defaults to 4.

Number of threads for worker.