Date: Thu, 29 Feb 1996 14:28:51 -0500
From: Mark Daly <mjdaly@genome.wi.mit.edu>
Subject: New version of MAPMAKER/SIBS (v 2.0)

A new version of MAPMAKER/SIBS is now available on the ftp site genome.wi.mit.edu in the subdirectory distribution/software/sibs

The new version is considerably faster, includes fixes to all known bugs, and adds some new features. If you are using previous versions, you should download this newer version.

Changes in MAPMAKER/SIBS version 1.1 -> 2.0

• (1) The new version includes algorithmic improvements that speed it up by a factor of 10-20 for large sibships with multiple affecteds.

• (2) A weighting is applied to sibships with multiple affecteds when the "all pairs" setting is used. Each pair from a sibship with N affecteds is weighted by 2/N. As a result, a sibship with N affecteds contributes N-1 (rather than N(N-1)/2) effective pairs. This weighting is designed to counteract the inflation of significance caused by statistical dependence among pairs from the same sibship. We recommend that either the "first pair" setting or the "all pairs" setting with the weighting be used in all analyses.

• (3) There is no longer a need to rescan when changing pair settings.

• (4) The dump_ibd command now works correctly for pedigrees with more than one affected/phenotyped pair. It reports the pedigree number, as well as the pair, to which the distribution applies.

• (5) The phenotype-based commands now work for X-linked data for all types of sibpairs, not just brother-brother. The analysis assumes that the difference in phenotype is a function of whether 0 or 1 alleles are inherited IBD from the mother, and makes no distinction between sibpair types.

• (6) We have fixed any other problems that have been brought to our attention. However, as always there is a chance that bugs remain or that new ones have been introduced. Please keep us informed should you encounter any. Send email to leonid@genome.wi.mit.edu, mpreeve@genome.wi.mit.edu, and mjdaly@genome.wi.mit.edu.