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Rare Variant Burden Testing
Upload data and run a gene-based rare variant test (local Docker MVP; TES-ready).
VCF/BCF + Sample Table
SKAT / Burden / SKAT-O
Covariate-aware
Run
Inputs
Upload files (stored under
data/uploads/rare_variant_burden/<run_id>/
).
VCF/BCF (required)
Prefer
.vcf.gz
(bgzip) with index.
VCF index (optional)
.tbi
for vcf.gz,
.csi
for bcf.
Sample table (required)
Must contain sample_id + phenotype + covariates columns.
Genome build
GRCh38
GRCh37
Optional GTF (for mapping if VCF not annotated)
If provided, mapping mode switches to GTF.
Phenotype & Covariates
Sample ID column
Phenotype type
Binary (case/control)
Quantitative
Phenotype column
Case value
Control value
Covariates (comma-separated)
MVP assumes numeric; we’ll add per-covariate typing next.
Annotation & Filters
Annotation field
CSQ (VEP)
ANN (SnpEff)
Gene key
Max MAF
Max missing rate
MVP uses pLoF mask by default. Next we’ll add full mask UI (missense, damaging scores, etc.).