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install-references

Download and configure reference files required by VNtyper 2.

By default, this command downloads verified pre-built bundles from berntpopp/vntyper-data. See Reference Setup for verification details and --from-source requirements.

Synopsis

vntyper [global-options] install-references
    -d <dir>
    [--skip-indexing]
    [-t <int>]
    [--aligners <aligner> ...]
    [--references <reference> ...]
    [--derive-only]
    [--from-source]
    [--release-spec <path>]

Arguments

Option Type Default Description
-d, --output-dir path (required) Destination path for reference installation
--skip-indexing flag off Skip BWA indexing (applies to --from-source; pre-built bundles re-index only on BWA version mismatches)
-t, --threads int 4 Indexing thread count (used during --from-source operations)
--aligners list bwa Aligners for which indices are built (bwa, bwa-mem2, minimap2). Only used with --from-source
--derive-only flag off Rebuild derived files (muc1_region_hg19.fa, muc1_region_hg38.fa, All_Pairwise_and_Self_Merged_MUC1_motifs_filtered.fa) from local files without downloading. Missing sources skip derivation and verify existing files in place. Cannot combine with --from-source
--references list hg19 hg38 Physical reference genomes to install: hg19, hg38, GRCh37, GRCh38, hg19_ensembl, hg38_ensembl
--from-source flag off Download and index chromosome FASTAs directly from primary sources instead of the release bundle. Requires seeds (MUC1_motifs_Rev_com.fa, code-adVNTR_RUs.fa, vntr_db_advntr_v2.zip, filter_config.json)
--release-spec path None File providing explicit source URLs and digests for release builds (requires --from-source)

Every run installs shared assets (MUC1 motif FASTAs and adVNTR databases) regardless of selected reference assemblies.

Examples

Install default reference set (hg19 and hg38 bundle):

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

Install all reference genomes:

vntyper install-references -d /path/to/refs --references hg19 hg38 GRCh37 GRCh38 hg19_ensembl hg38_ensembl

Install a single assembly:

vntyper install-references -d /path/to/refs --references hg19

Rebuild from upstream sources with multiple aligner indices:

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

Update custom configuration to point to installed references:

vntyper --config-path /path/to/config.json install-references -d /path/to/refs