indexgvcf

This tool creates an index for a VCF(vcf.gz) or GVCF(g.vcf/g.vcf.gz) file. The index file name is determined by appending .tbi to the name of the vcf.gz/g.vcf.gz file, or .idx to the name of the g.vcf file being indexed, and is created in the same directory as the VCF/GVCF file itself.

Please note that haplotypecaller and deepvariant also write the index file when generating a .gz output.

Refer to the indexgvcf Reference section for a detailed listing of all available options.

Quick Start

# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \
    pbrun indexgvcf \
    --input /workdir/${INPUT_GVCF}

Compatible CPU GATK4 Command

$ gatk IndexFeatureFile -I <INPUT_DIR>/${INPUT_GVCF}

Options