MegaVCF Explorer - PGx Pipeline

Database Evidence Coverage

Top Drug Contexts

Functional Impact

Variant Browser

Import comments

CNV key:CNV consensusCNV review

✓	Status	Type	CNV state	Length	Gene	Variant	Patients	Consequence	Impact	ACMG	Evidence criteria	PGx drugs	DB hits	gnomAD AF	ClinVar	Comments

Gene-Centric View

Gene	Variants	Known	High/Moderate	Top evidence

Genome Map

Every variant found, placed on its chromosome (GRCh38). Colour shows predicted impact; CNVs are wider marks. Hover a marker for details and click it to open it in the Variant Browser, or click a chromosome to zoom in — clustered variants are spread into stacked lanes so each is distinct. Per-database evidence counts remain on the Overview tab.

Pharmacogenomic Diplotypes

Per-sample star-allele diplotypes with the resulting metaboliser phenotype, activity score, calling source (Cyrius for CYP2D6 when available, otherwise PyPGx), call status, and CPIC drug guidance. Research use only.

Sample	Gene	Diplotype	Phenotype	Activity	Source	Status	Notes	CPIC drug guidance

Clinical / PGx View

Gene	Variant	Type	Impact	ACMG	Criteria	PGx drugs	PharmGKB	CPIC	DPWG	PharmVar	ClinVar	LOVD	Splice

Sample Genotype Matrix

The matrix is intentionally limited to the highest-priority variants so it remains readable. Cells show GT calls from the Mega VCF: reference, heterozygous/non-reference, homozygous alternate, or missing.

How This Explorer Is Calculated

The pipeline first builds the Mega VCF by adding VEP annotations, PGx prioritization, database enrichment, case-control statistics, HWE/QC flags, splice evidence, and CNV context as INFO fields where available.

This explorer is generated from the enriched and prioritized tables because those contain researcher-readable columns. In the browser, repeated patient-level rows with the same CHROM/POS/REF/ALT allele are compacted into expandable variant stacks. SNV/indel rows are expanded from MegaVCF genotypes so carrier patients remain visible. CNV rows are added from the consensus CNV interval table and include sample, class, interval, and length when available. Known status is assigned when an allele-aware source contributes evidence, such as dbSNP, remote Ensembl colocated variant evidence, PharmGKB variant-level evidence, PharmVar, ClinVar, gnomAD, or LOVD. For CNVs, PGx gene-drug evidence from PharmGKB, CPIC, and DPWG also marks the CNV as known.

Gene-level sources such as CPIC, DPWG, Reactome, DrugBank, OMIM, ClinGen, and ClinPGx are shown as interpretation context. For SNVs/indels they are context unless an allele-level source is also present; for CNVs, PGx gene-drug evidence is treated as known CNV context.