VCF2GENOMICSDB(1) | User Commands | VCF2GENOMICSDB(1) |
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
July 2022 | vcf2genomicsdb |