GVCF PROCESSING¶

Accelerated processing of g.vcf files

INDEX GVCF¶

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

$ pbrun indexgvcf --input input.g.vcf

$ gatk IndexFeatureFile -F input.g.vcf

--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.

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

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

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

--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.