vcf2genomicsdb_init - workspace initializer for GenomicsDB
vcf2genomicsdb_init [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