NAME¶

vcf2genomicsdb - VCF data converter for GenomicsDB

SYNOPSIS¶

vcf2genomicsdb [options] <loader_json_config_file>

OPTIONS¶

--help, -h

--version

--progress, -p

Show import progress

specify minimum amount of time between progress messages with --progress=<interval> or -p<interval> where <interval> is a floating point number. Default units are seconds, explicitly specify seconds, minutes, or hours by appending s, m, or h to the end of the number

--tmp-directory, -T

Specify temporary directory (stores some temporary files during the import process, default is /tmp)

--rank, -r

Manually assign MPI rank of process, determines on which partition the process will operate

--split-files

Split the files specified by the callset mapping JSON file according to the column partitions in the loader JSON

resulting files will be placed in the same directory as the originals default behavior is to generate split files only for the partition corresponding to the rank

Modifiers to --split-files:

--split-all-partitions Overrides --split-files default behavior and instead creates split files for all partitions --split-files-results-directory Specify where to place split files, overrides default behavior of placing them in the same directory as originals --split-output-filename Create a split file for one column partition and one VCF

e.g. vcf2genomicsdb <loader.json> --rank=<rank> --split-files --split-output-filename=<output_path> <input.vcf.gz>

--split-callset-mapping-file

Create callset mapping files containing the paths to the generated split files, one callset per partition