---
name: "gt_mpi_gather"
section: "1"
platform: "linux"
package: "genomicsdb-tools"
version: "1.4.4-3"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/gt_mpi_gather"
---

# gt\_mpi\_gather(1)

MPI gatherer for GenomicsDB

## 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\> \[\<other\_args\>\]