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

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