Forensic & FIGG Genotyping

WOPR — Robust genotyping for challenging, low-coverage samples

WOPR is a validated end-to-end bioinformatics pipeline that converts highly degraded or low-coverage forensic sequencing data—including newly generated or previously sequenced FASTQ files—into actionable SNP genotype profiles optimized for forensic investigative genetic genealogy (FIGG). The pipeline is validated against industry standards and routine casework samples to ensure reproducibility, traceability, and reporting readiness.

Works on challenging sample types

Handles rootless hair, bone, and other degraded forensic specimens.
Designed to rescue short or damaged reads (adapter trimming, read merging, robust alignment).

High performance on low / damaged DNA

Produces usable SNP profiles from very low coverage—usable profiles at coverage levels as low as 0.1×.
Calls up to ~1.5M SNPs (union of common DTC/consumer arrays) when sequencing depth permits.

Validated & auditable

Containerized software, version tracking, and per-run metadata for reproducibility and audit trails.

FIGG-ready outputs

Generates genotype files optimized for GEDmatch / FTDNA upload and searching. WOPR includes genotype refinement and filters to maximize usable matches while removing poor-quality or “matchy” files.

Quality controls & reporting

Comprehensive QC dashboards and per-sample PDF reports (coverage, duplication, endogenous content, etc.).
Automated sex estimation, mixture detection, mitochondrial and Y-DNA haplogroup calls.

Designed for reliable database matching

Targets a minimum of ~460K called SNPs for reliable GEDmatch searching (empirical validation).
Flags or removes samples that fail heterozygosity or quality thresholds to prevent misleading matches.

Validation highlights

**Figure 1. Single-library SNP recovery across low-coverage forensic samples.** Number of SNPs recovered as a function of mean sequencing coverage for single-library bone and hair samples processed with WOPR. Usable SNP profiles are generated at coverage levels as low as ~0.1×, with recovery increasing predictably as coverage increases, supporting reliable downstream forensic genetic genealogy analysis.

WOPR concordance versus mean coverage relative to GIAB truth genotypes — **Figure 2. WOPR genotype concordance relative to GIAB truth genotypes.** Concordance with Genome in a Bottle (GIAB) truth genotypes as a function of mean sequencing coverage across multiple reference samples. High concordance is maintained even at low coverage, with values approaching saturation as coverage increases, demonstrating the robustness of WOPR genotyping from limited or degraded sequencing data.