NAME

       gt_mpi_gather - MPI gatherer for GenomicsDB

SYNOPSIS

       gt_mpi_gather [options]

OPTIONS

              --help, -h

              Print a usage message summarizing options available and exit

              --json-config=<query json file>, -j <query json file>

              Can   specify   workspace,   array,   query_column_ranges,   query_row_ranges,   vid_mapping_file,
              callset_mapping_file, query_attributes, query_filter, reference_genome, etc. as fields in the json
              file e.g.

       { "workspace" : "/tmp/ws",
              "array" : "t0_1_2", "query_column_ranges" : [ [ [0, 100 ], 500 ] ], "query_row_ranges" : [ [ [0, 2
              ]     ],     "vid_mapping_file"      :      "/tests/inputs/vid.json",      "callset_mapping_file":
              "/tests/inputs/callset_mapping.json",  "query_attributes"  : [ "REF", "ALT", "BaseQRankSum", "MQ",
              "MQ0", "ClippingRankSum", "MQRankSum", "ReadPosRankSum",  "DP",  "GT",  "GQ",  "SB",  "AD",  "PL",
              "DP_FORMAT", "MIN_DP" ] }

              --loader-json-config=<loader json file>, -l <loader json file>

              Optional, if vid_mapping_file and callset_mapping_file fields are specified in the query json file

              --workspace=<workspace dir>, -w <GenomicsDB workspace dir>

              Optional, if workspace is specified in any of the json config files

              --array=<array dir>, -A <GenomicsDB array dir>

              Optional, if array is specified in any of the json config files

              --print-calls

              Optional, prints VariantCalls in a JSON format

              --print-csv

              Optional,  outputs  CSV  with  the  fields  and  the  order  of  CSV lines determined by the query
              attributes

              --produce-Broad-GVCF

              Optional, produces combined gVCF from the GenomicsDB data constrained by the  query  configuration
              --output-format=<output_format>, -O <output_format>

       used with --produce-Broad-GVCF
              Output  format can be one of the following strings: "z[0-9]" (compressed VCF),"b[0-9]" (compressed
              BCF) or "bu" (uncompressed BCF). Default is uncompressed VCF if not specified.

              --produce-histogram

              Optional

              --produce-interesting-positions

              Optional

              --version Print version and exit

              If none of the print/produce arguments are specified, the tool prints all the Variants constrained
              by the query configuration in a JSON format

              Parallel Querying

              MPI could be used for parallel querying, e.g.   mpirun  -n  <num_processes>  -hostfile  <hostfile>
              ./bin/gt_mpi_gather -j <query.json> -l <loader.json> [<other_args>]

gt_mpi_gather                                       July 2022                                   GT_MPI_GATHER(1)