I'm hoping that someone can give some advice a a linkage program that will handle a large number of markers and a reasonably large pedigree. The markers are from the illumina linkage chip , or HT-sequencing. The old favourite Merlin can't handle this problem, even if the pedigree is broken up and marker set reduced to a single chromosome. Thanks in advance Paul [[alternative HTML version deleted]]

On Sun, Aug 22, 2010 at 7:35 PM, Paul Leo <p.leo@uq.edu.au> wrote: > I'm hoping that someone can give some advice a a linkage program that > will handle a large number of markers and a reasonably large pedigree. > The markers are from the illumina linkage chip , or HT-sequencing. The > old favourite Merlin can't handle this problem, even if the pedigree is > broken up and marker set reduced to a single chromosome. > > You could look into Simwalk; it has its own limitations (I think 1000 snps, but I could be wrong), but it will handle large pedigrees since it used Gibbs sampling rather than full likelihood space calculations. Sean [[alternative HTML version deleted]]