Uploading a VCF File

Supported Formats

Helix Insight accepts VCF files in version 4.1 and 4.2 format, either as plain text (.vcf) or bgzipped (.vcf.gz). Whole genome sequencing files containing approximately 4 million variants (1-2 GB compressed) are fully supported.

Genome Build Requirement

GRCh38 (hg38) is the primary genome build. GRCh37 (hg19) files are also accepted -- the platform performs automatic liftover to GRCh38 during upload, so no manual conversion is required. The liftover step is transparent and reported in the processing summary.

Single-Sample Analysis

Helix Insight currently supports single-sample VCF files. If your file contains multiple samples, extract the sample of interest using a tool such as bcftools before uploading. Trio analysis (proband plus parents) is on the development roadmap.

What Happens After Upload

Once the file is uploaded, it is validated for format compliance and the processing pipeline begins automatically. The six-stage pipeline parses the VCF, applies quality filtering, annotates variants with Ensembl VEP, enriches them with reference database data, classifies each variant using the ACMG framework, and exports the results for clinical review.

Expected chromosomes are chr1 through chr22, chrX, chrY, and chrM. Non-standard contigs such as decoys, alternative haplotypes, and unplaced scaffolds are skipped, with a count reported in the processing summary.