Haplogrep

Haplogrep classifies human mitochondrial DNA sequences into haplogroups and provides computational annotations and summary statistics to support population, medical, and forensic analyses.

Key Features:

• Enhanced Data Handling Capabilities: Optimized data handling for large-scale biobank datasets enabling analysis of thousands of samples.
• Comprehensive Haplogroup Summary Statistics and Variant Annotations: Integration of haplogroup summary statistics and variant annotations from publicly available genome databases.
• Flexible Phylogenetic Tree Integration: Support for importing and integrating custom phylogenetic trees for classification.
• Improved FASTA Classification Algorithms: Algorithmic adaptations for FASTA classification incorporating BWA-specific alignment rules.
• Pre-Classification Quality Control for VCF Samples: Pre-classification quality-control procedures specific to Variant Call Format (VCF) samples.

Scientific Applications:

• Medical Research: Analysis of mitochondrial haplogroups to study genetic predispositions and disease associations.
• Forensic Science: Haplogroup-based individual identification and ancestry inference from mitochondrial DNA.
• Evolutionary Biology: Investigation of human migration patterns and population structure via mitochondrial DNA variation.

Methodology:

Support for multiple file formats including VCF and FASTA; algorithmic adaptations for FASTA classification using BWA-specific alignment rules; pre-classification quality control for VCF samples; integration of variant annotations and haplogroup summary statistics from public genome databases; and import/integration of phylogenetic trees for classification of large-scale datasets.