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HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
1Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK. r.farrer@exeter.ac.uk.
BMC Bioinformatics
|November 23, 2021
Summary
HaplotypeTools is a new software tool that accurately phases variant sites in complex genomes. It aids in analyzing hybrid genomes and identifying parental ancestry for specific genomic regions.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Haplotype identification is crucial for analyzing diploid and polyploid genomes.
- Existing tools for physical phasing and downstream analysis are limited.
Purpose of the Study:
- Introduce HaplotypeTools, a novel software suite for haplotype phasing and analysis.
- Provide a tool for downstream analysis of phased variant data.
Main Methods:
- Phasing variants using VCF and BAM files by identifying overlapping reads.
- Extending phased regions using additional reads, with parallel processing capabilities.
- Utilizing utility scripts for crossover detection and phylogenetic placement of haplotypes.
Main Results:
- HaplotypeTools demonstrated higher accuracy than WhatsHap on simulated data.
- Accurate phasing and ancestry determination for the hybrid fungal isolate *Batrachochytrium dendrobatidis* (Bd) SA-EC3.
- Identified parental lineages BdGPL and BdCAPE for 80% of haplotypes in Bd SA-EC3, with high phasing conservation.
Conclusions:
- HaplotypeTools is a valuable resource for analyzing hybrid and recombinant genomes.
- Enables precise identification of parental ancestry in sub-genomic regions.
- Facilitates advanced genomic analyses in diploid and polyploid organisms.
