GVCF PROCESSING

Accelerated processing of g.vcf files

INDEX GVCF

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

QUICK START

$ pbrun indexgvcf --input input.g.vcf

COMPATIBLE CPU GATK4 COMMAND

$ gatk IndexFeatureFile -F input.g.vcf

OPTIONS

--input

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

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory where bin/ and species/ folders are located.

--keep-tmp

Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in installation directory.

--version

View compatible software versions.

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

--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.

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory where bin/ and species/ folders are located.

--keep-tmp

Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in installation directory.

--version

View compatible software versions.