Hapi (short for Haplotyping with imperfect genotype data) is a novel easy-to-use, R package for 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.
|Author||Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, Le Zhang, Julong Wei, Sergio Pietro Ferrante, Mikeal L. Roose, Zhenyu Jia|
|Bioconductor views||Genetics GenomicVariation HiddenMarkovModel Microarray SNP Sequencing SingleCell|
|Maintainer||Ruidong Li <[email protected]>|
|Package repository||View on GitHub|
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