Hi all, I am about to get back into a project re runs of homozygosity. This summer I used the Affy CNV algorithm, which used HMMC to determine whether a given SNP was within a homozygous run. I have since seen the Double Helix has an algorithm as well - although it seems simpler than the Affy one (which in itself is not a bad thing, but I don't think that the Double Helix algorithm is 'forgiving' of heterozgote calls that exist in a long stretch of homozygotes and that are therefore probably errors). But I'd much rather use R than a proprietary software package. So is anyone here aware of a way to judge runs of homozygosity in 100 or 500K SNP data using R or Bioconductor? If so, what type of algorithm is used? Thanks in advance, Matt -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.com