Question about sample data...

[CholoTook]

Hello,

I have SNP-Chip data from 8000 (non human) samples. Am I right in thinking that if I pass this SNP data to haploSep, it will show me the haplotype structure of individuals?

Sorry if this is a stupid question, I'm just trying to get to grips with how to take population genotype data and turn it into knowledge about recombination in the population.

Cheers,
Dan.

[MartaPelizzola]

Hi Dan,

I am very sorry for the late answer. I hope this may still be helpful.

I am not very familiar with SNP-Chip data, but I think it should work if you have multiple data samples for the same group of individuals. How do your data look like exactly?

Best wishes,
Marta

[CholoTook]

Thanks Marta,

Yes, that's right. Within the 8,000 samples there are about 100 groups, i.e. different cultivars of a plant species. The actual number of samples per group varies a lot, so for some groups there isn't good statistics on allele frequency, but for others there should be.

Our SNP-Chip data gives us the exact allele for each sample at a set of about 100,000 loci across the 5Gbp genome.

We have the data in PLINK format.

Cheers,
Dan.