GVCF PROCESSING
Accelerated processing of g.vcf files
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
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --version
Full path to the directory where temporary files will be stored.
Full path to the PetaGene installation directory where bin/ and species/ folders are located.
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in installation directory.
View compatible software versions.
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
- --in-gvcf
- --in-selectvariants-dir
- --out-vcf
- --num-threads
(required) Input Reference file in fasta format.
Input g.vcf file that will be converted to VCF. Required if --in-selectvariants-dir
is not specified.
Path to the output directory of selectvariants. Required if –in-gvcf is not specified.
(required) Output VCF file.
Defaults to 4.
Number of threads for worker.
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --version
Full path to the directory where temporary files will be stored.
Full path to the PetaGene installation directory where bin/ and species/ folders are located.
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in installation directory.
View compatible software versions.