I was looking for help on how to use data from 240S Illumina chips for
linkage. I ran a family on these chips which genotype 240,000 SNPs
across the genome. Unfortunately none of the linkage programs that I
have looked at are able to handle this amount of data. Even SNPlink
which is designed to cut down the large numbers of SNPs does not work
with such a large dataset. One approach that I was thinking of following
is to match the SNPs on Illumina's linkage panel V to the SNPs that I
have generated using the 240S SNP chip. Problem is that not all of the
linkage panel V SNPs are on the 240S Illumina SNP chip, so I may have to
take nearby SNPs. My questions are as follows:
(1) Has anyone any experience with using 240S or 550K Illumina SNP
chips for linkage studies?
(2) Does anyone have a list of SNPs on the 240S SNP chip that they
know work for linkage?
Many thanks in advance,
Best,
Bryan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.bio.net/bionet/mm/gen-link/attachments/20070824/4ea11b64/attachment.html
