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.
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.