MartaPelizzola/haploSep

Question about sample data...

Opened this issue · 2 comments

CholoTook commented

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 commented

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 commented

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.