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

vcf2genomicsdb_init                                 July 2022                             VCF2GENOMICSDB_INIT(1)