Phase 11 · Sample & cohort analysis

Multi-sample VCF → Cohort Prioritization

Keep the sample dimension of a VCF: inspect GT, DP, AD, GQ and VAF, compare samples or study groups, annotate variants through the Phase 8 engine, and send selected alleles into the full Variant → Experiment workflow.

Research scope: trio, tumor/normal and case/control candidate flags are transparent prioritization heuristics. They do not establish inheritance, somatic status, pathogenicity or clinical actionability without independent validation.

1. Load a multi-sample VCF

VCF file

Genome assembly

Safety ceiling

VCF text

No cohort parsed yet.

2. Samples & study roles

Samples0

Variant alleles0

Genotype cells0

Carrier calls0

Annotated0

Candidates0

Minimum DP

Minimum GQ

Minimum carrier VAF

Assign sample roles, then annotate and/or infer study-design candidates.

3. Cohort variant table

Sample

Genotype

Candidate

Consequence

Max gnomAD AF

	Variant	Gene / consequence	Carriers	Sample calls	ClinVar / AF	Cohort signal	Evidence	Workflow

4. Sample × variant matrix

Cells show genotype, depth and VAF for the current filtered variants. Horizontal scrolling is expected for larger cohorts.