HaploTypo

HaploTypo maps genetic variants to haplotypes using phased reference genomes to infer haplotype correspondence for heterozygous variants and generate per-haplotype FASTA sequences.

Key Features:

• Phased Genome Utilization: Leverages phased reference genomes to resolve the arrangement of alleles on each chromosome.
• Haplotype Correspondence Inference: Determines haplotype correspondence for heterozygous variants to assign alleles to specific haplotypes.
• Independent FASTA File Generation: Produces two independent FASTA files representing reconstructed haplotype sequences for diploid organisms.
• Implementation: Implemented in Python 2.7 and Python 3.5.

Scientific Applications:

• Population genetics: Enables haplotype-resolved analyses by assigning variants to haplotypes for population-level studies.
• Evolutionary biology: Facilitates study of inheritance patterns and haplotype structure in evolutionary analyses.
• Personalized medicine: Supports investigation of haplotype-specific functional implications and associations with phenotypic traits or diseases.

Methodology:

Uses phased reference genomes to infer haplotype correspondence for heterozygous variants and outputs two per-haplotype FASTA files; implemented in Python 2.7 and Python 3.5.