VCF meta-info
vcf_metainfoDetermine a VCF file's genome build, variant input type (WGS/array/gVCF), and inferred genetic ancestry to guide PRS scoring. Use this to validate inputs before computing polygenic risk scores.
Instructions
Detect a genome's build, input type (WGS/array/gVCF), and genetic ancestry.
One call that pairs WGS-vs-array/gVCF detection with population (super-population) inference, so before scoring you already know: the genome build (read from the VCF header), whether the input is whole-genome sequencing, a consumer genotyping array (and which chip), or a gVCF / all-sites callset, and the sample's inferred super-population.
Pass genotypes_path (a normalized Parquet from normalize_vcf /
download_sample_genome) for the fast path, or a raw vcf_path.
Genome-build detection reads the VCF header, so it is only available on the
vcf_path branch.
The result carries ready-to-use recommendations:
recommended_reference_restoration (feed to compute_prs /
compute_prs_batch / compute_prs_by_trait as reference_restoration
— though those tools default to "auto" and derive the same thing) and
recommended_superpopulation (feed as superpopulation). Set
infer_population=False to skip ancestry inference (it pulls a small model
from HuggingFace on first use).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| panel | No | ||
| vcf_path | No | ||
| resolution | No | superpop | |
| genome_build | No | ||
| genotypes_path | No | ||
| infer_population | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| path | Yes | Genotype source inspected (VCF or normalized Parquet). | |
| chip_id | No | Detected genotyping-array chip id (array input only). | |
| is_gvcf | No | True when reference-block / all-sites (gVCF) records were detected. | |
| summary | Yes | Human-readable summary of the detected properties. | |
| warnings | No | Non-fatal caveats (e.g. ancestry inference skipped). | |
| input_type | Yes | Detected input kind: 'wgs', 'genotyping_array', or 'unknown'. | |
| n_variants | Yes | Number of variant rows in the genotype source. | |
| marker_count | Yes | Variant/marker count used for the input-type call. | |
| chip_platform | No | Detected chip platform label (array input only). | |
| ancestry_error | No | Why ancestry inference was skipped/failed, if it was. | |
| ancestry_panel | No | Reference panel used for ancestry inference (e.g. '1000g'). | |
| fine_population | No | Finer population call when resolution='population'. | |
| superpopulation | No | Inferred super-population (AFR/AMR/EAS/EUR/SAS), or null if not inferred. | |
| ancestry_coverage | No | Fraction of the ancestry model's sites covered by the sample. | |
| ancestry_confidence | No | Classifier confidence for the super-population call (0-1). | |
| genotype_input_mode | Yes | Resolved genotype interpretation: 'variant_only', 'all_sites', or 'plink_present_only'. | |
| chip_generation_label | No | Detected chip generation label (array input only). | |
| detected_genome_build | No | Genome build read from the VCF header ('GRCh37'/'GRCh38'), or null. | |
| ancestry_probabilities | No | Per-super-population classifier posteriors. | |
| n_variants_ancestry_used | No | Number of sample variants used by the ancestry model. | |
| recommended_superpopulation | No | Super-population to pass to percentile / compute_prs_by_trait, when inferred. | |
| recommended_reference_restoration | Yes | Scope to pass as compute_prs* reference_restoration: 'wgs', a chip id, or 'off'. |