Snp Selection For Genotyping

Question

[blacktomato27]

Hi to all,

I have data like this,

Assay  Genetic pos  Physical pos  %poly       chr#
134    0.3           408068           0          1
491    0            4259452         100          1
1709  25.8           900596          47          1
1641  27.3          1239146          37          1
488    0.0          2276961          74          1

Like this i have data for 12 chromosomes more or less 100 SNPs per chromosome, now i want to select 10 per chromosome to run on my material but i do not know how to select them to get 100% reliable results. Can any one help me or provide guidelines to select SNPS for the above condition. Any help would be appreciated :)

Thanks in advance

Regards,

[zx8754]

You question is not clear, maybe have a look at SNP Tagger.

Answer 1

[Vitis]

If you're selecting SNP markers for genetic mapping, you need to space them evenly on the chromosome in terms of genetic distances (in cM). Usually I would pick two or three SNPs around a selected position and design markers and test them. So for each selected position, you could make sure there is one working marker. The testing process can be tedious as sometimes at certain position no good marker would work, in that case you may need to go back and pick SNP and make markers again. But once you've got a fixed set of reliable markers (like you said, 10 per chromosome), they will be there and work all the times. If you're designing CAPS markers, you may be able to automate the process by chaining together blast, clustalw and CAPS designer using perl.