install-references¶

Download and set up the reference files required by VNtyper 2.

Synopsis¶

vntyper [global-options] install-references
    -d <dir>
    [--skip-indexing]
    [-t <int>]
    [--aligners <aligner> ...]
    [--references <reference> ...]

Arguments¶

Option	Type	Default	Description
`-d, --output-dir`	path	(required)	Directory where references will be installed
`--skip-indexing`	flag	off	Skip the indexing step
`-t, --threads`	int	`4`	Number of threads to use for indexing
`--aligners`	list	`bwa` only	Specific aligners to use (e.g., `bwa`, `bwa-mem2`, `minimap2`). If not specified, only BWA is used
`--references`	list	`hg19 hg38`	Specific references to process (e.g., `hg19`, `hg38`, `GRCh37`, `GRCh38`). Default: UCSC references only (hg19, hg38)

Examples¶

Install references with default settings:

vntyper install-references -d /path/to/refs

Install with multiple aligners and 8 threads:

vntyper install-references -d /path/to/refs --aligners bwa bwa-mem2 -t 8

Install specific references without indexing:

vntyper install-references -d /path/to/refs --references GRCh37 GRCh38 --skip-indexing