Uploading a VCF File

Supported Formats

Folklore 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 Samples and Families

Primary analysis accepts one sample per VCF. Multi-sample VCF files should be split before upload. For family analysis, process the proband, parents, and optional siblings separately, then link the resulting cases in the Family Analysis module for relationship QC, de novo review, compound-heterozygous phasing, and segregation evidence.

See Family Analysis Methodology.

What Happens After Upload

Once uploaded, the file is checked for format and genome-build compatibility. The core path parses and quality-checks the variants, runs local annotation and reference enrichment, applies the relevant classifier, and stores the evidence for clinical review. Variants on chrM and supported structural-variant records are routed to their dedicated interpretation modules.

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.