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

vcf2genomicsdb                                      July 2022                                  VCF2GENOMICSDB(1)