Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells
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Convert genotype coded in A/T/C/G to 0/1
Hapi is a novel easy-to-use package that only requires 3 to 5 gametes ...
Consensus haplotype assembly
Assembly of haplotypes in regions at the end of a chromosome
Automatic inference of haplotypes
Maximum Parsimony of Recombination (MPR) for proofreading of draft hap...
Filter out hetSNPs in potential complex regions
Histogram of crossover distance
Visualization of crossover map
Histogram of crossover resolution
Filter out hetSNPs with potential genotyping errors
Selection of hetSNPs to form a framework
Visualization of haplotypes in a single gamete cell
Indentify crossovers in gamete cells
Imputation of missing genotypes in the framework
Phase draft haplotypes by majority voting
Convert genotype coded in 0/1 to A/T/C/G
Inference of chromosome-length haplotypes using a few haploid gametes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.