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