Haplotype phasing for non-human model organism

Question

[kirannbishwa01]

I am planning to do haplotype phasing for a plant model using genome resequence data which only has reference genome. I was thinking of using IMPUTE2, BEAGLE or SHAPEit but these programs require several supporting map and gene files. But, no such data is available for my model.

I only have 1) reference genomes 2) polymorphism data (snp, indels in *.vcf file) and 3) bam file alignment from a genome resequenced data (which was used to generate the vcf's). I have gone through the manuals of these programs but I am not sure how I may be able to generate other required file. I have started working on beagle with example data and my vcf file but lot of the parameters that are required for my data are missing. It seems like the amount of resources I have isnot enough for phasing.

How can use use this limited resource to do genotype/haplotype phasing. Also, I only have 6 individuals /population for two different population.

Could someone share their insights and experience?

Thanks in advance !

Answer 1

[Zev.Kronenberg]

The accuracy of statical phasing methods are correlated with the number of genomes sequence, recombination rates, and effective population size. You do not have enough samples to get reliable phasing.

[kirannbishwa01]

Thanks for the info Zev. I understand I have small sample size, but could there be a way to do any test of selection using this genome level data. I have checked around but not find anything good to use. Any suggestions is appreciated !

Thanks,

[bouchenak.chuxi]

Hello, I'm currently facing the same issue with my plant model, any feedback, or recommendations? I thought of using WhatsHap but not sure to what level that would be accurate.