GVCF PROCESSING OVERVIEW

Accelerated processing of g.vcf files

This tool creates an index for vcf/g.vcf/g.vcf.gz files.

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$ pbrun indexgvcf --input input.g.vcf


COMPATIBLE CPU GATK4 COMMAND

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$ gatk IndexFeatureFile -F input.g.vcf


OPTIONS

--input

(required) Path to the vcf/g.vcf/g.vcf.gz file to be indexed.

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

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


COMPATIBLE CPU GATK4 COMMAND

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


OPTIONS

--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.

© Copyright 2020, NVIDIA. Last updated on Sep 14, 2020.