k8hertweck
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Lightning talk: "phASE-Stitcher: A tool for phasing genome wide haplotype in F1 hybrids using Phase Informative Reads"
Authors: Bishwa K. Giri, Dr. David L. Remington Abstract: Next gen sequencing data has provided breakthrough in mining the genetics variants in lots of organism either model or non-model. However, next level of problem is in tying these variants in a set of haplotypes which could provide strong data for population genetics, genomics and other studies. While lots of methods have been proposed to identify the most probably haplotype states using a large dataset, there is still a paucity of tools that can provide accurate haplotype in hybrid individuals. Additionally, hybrids and mixed population are highly heterozygote in nature, so inaccurate configuration of phase states of the alleles in hybrids or mixed parental population can lead to misrepresentation of the actually biology occurring in the organism. Here we present a method and tool that takes the readback phased state of the alleles from next generation sequence data and segregates them into probable population haplotype using the frequency of the alleles in the parental population. We also introduce first order markov model to improve the accuracy of the phase states. This method/tool can be use to prepare the genome wide haplotype of the hybrid individuals, population level reference genome panels and preparation of more accurate diploid genome of an individual. The discussed tool can be found here.