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edits
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--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)
--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)
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== How It Works ==
For each possible position, glfMultiples considers a series of potential polymorphisms, including transitions and transversions from the reference base, but also bi-allelic polymorphisms where neither of the alleles present in the sample is the reference base. For each potential polymorphism type, the likelihood of the observed bases is maximized with respect to allele frequency. Decisions of which sites are polymorphic take into account the maximized likelihood but also an overall prior for each type of polymorphism (for example, transitions are assumed to account for ~2/3 of all variants).
glfMultiples works with log-likelihoods internally to avoid underflows in samples that may include hundreds or thousands of individuals.
== Download ==
== Download ==
The current version is available for download from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-05-25.tar.gz here].
The current version is available for download from http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-06-16.tar.gz.
== TODO ==
== TODO ==
