---
name: "vcf2genomicsdb_init"
section: "1"
platform: "linux"
package: "genomicsdb-tools"
version: "1.4.4-3"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf2genomicsdb_init"
---

# vcf2genomicsdb\_init(1)

workspace initializer for GenomicsDB

## NAME

vcf2genomicsdb\_init - workspace initializer for GenomicsDB

## SYNOPSIS

**vcf2genomicsdb\_init** \[*options*\]

## OPTIONS

-

  \--help, -h

-

  Print a usage message summarizing options available and exit

-

  \--workspace=\<GenomicsDB workspace URI\>, -w \<GenomicsDB workspace URI\>

-

  If workspace does not exist, it is created first exits if workspace exists and is invoked without the overwrite-workspace option

-

  \--overwrite-workspace, -o

-

  Allow for workspace json artifacts to be overwritten

-

  \--sample-list=\<sample list\>, -s \<sample list file\>

-

  Specify sample URIs for import, one line per sample path

-

  \--samples-dir=\<folder to samples\>, -S \<folder to samples\>

-

  Specify Folder URI containing samples. Only vcf.gz/bcf.gz compressed samples are considered

-

  \--interval-list=\<genomic interval list\>, -i \<genomic interval list file\>

-

  Optional, create array partitions from intervals in interval list, one line per interval, default is partition by chromosome/contig, overrides **--number-of-array-partitions** and **--size-of-array-partitions**

-

  \--number-of-array-partitions=\<number\>, -n \<number\>

-

  Optional, suggested number of array partitions. Usually, the partitioning is per contig But, if this is 0, only a single array is created for the entire genomic space and it overrides all other partition specific command arguments

-

  \--size-of-array-partitions=\<size\>, -z \<size\>

-

  Optional, suggested size of arrays partitions, overrides **--number-of-array-partitions**

-

  \--merge-small-contigs, -m

-

  Optional, default is false and any contig smaller than ~1M will be merged into scaffolds

-

  \--include-fields=\<fields\>, -f \<fields\>

-

  Optional, Include only fields(comma-separated) listed in this argument while generating the vidmap default is to include all fields found in the vcf headers

-

  \--template-loader-json=\<template file\>, -t \<template file\>

-

  Optional, specify a template loader json file to use as a basis with loader json files

-

  \--append-samples, -a

-

  Optional, if specified, callsets will be appended with the new samples and lb\_row\_idx set to the new starting row. Note that the workspace and vidmap/callset/loader jsons should already exist and that the interval list, number and size of partitions and merge small contigs options are ignored with append samples

-

  \--verbose, -v

-

  Allow verbose messages to be logged

-

  \--version Print version and exit