HaplotypeTools

HaplotypeTools performs haplotype phasing and analysis using Variant Call Format (VCF) and Binary Alignment Map (BAM) files to enable physical phasing of variant sites in diploid and polyploid genomes.

Key Features:

• Phasing methodology: Identifies reads that overlap two or more heterozygous positions and extends phase groups by incorporating additional reads.
• Parallel execution: Phasing computation is optimized for parallel execution across computer clusters.
• Utility scripts for downstream analysis: Provides scripts for crossover detection and phylogenetic placement of haplotypes relative to other lineages or species.
• Accuracy and comparative performance: In comparisons with WhatsHap using simulated short and long reads, HaplotypeTools showed superior accuracy while producing slightly shorter haplotype lengths.
• Empirical application to Illumina data: Applied to Illumina data from a hybrid Batrachochytrium dendrobatidis isolate (SA-EC3), finding 80% of haplotypes clustered with parental lineages BdGPL (39%) and BdCAPE (41%), and ~99% phasing conservation between overlapping phase groups with either parental lineage, consistent with mitotic gene conversion or parasexuality.

Scientific Applications:

• Hybrid and recombinant genome analysis: Enables detection and characterization of hybrid or recombinant genomic regions in diploid and polyploid organisms.
• Parental ancestry assignment: Assigns parental lineage to sub-genomic regions using phased haplotypes and phylogenetic placement.
• Crossover detection and phylogenetic analysis: Supports identification of crossover events and phylogenetic placement of haplotypes to inform evolutionary relationships.

Methodology:

Operates on VCF and BAM files, identifying reads that overlap two or more heterozygous positions and extending phase groups by incorporating additional reads; the phasing computation is implemented to run in parallel across computer clusters and includes utility scripts for crossover detection and phylogenetic placement.