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covld

Estimate linkage disequilibrium between unphased loci

The software in this directory implements a method for estimating linkage disequilibrium, which is described in the following publication.

@Article{Rogers:G-182-839,
  author =       {Rogers, Alan R. and Chad Huff},
  title =        {Linkage Disequilibrium between Loci of Unknown Phase},
  journal =      {Genetics},
  year =         2009,
  volume =   182,
  number =   3,
  pages =    {839--844},
  month =    {July},
}

FILE                 DESCRIPTION

estimate_ld.py      Implements various estimators of LD.  If you write your
                    own Python program, import this as a package.

myexcept.py         Defines exceptions used by the other programs.

tst_r.py            Tests the functions in estimate_ld.py.

covld.py            Reads a data file and estimates LD using the Rogers-Huff
                    method and (optionally) the Excoffier-Slatkin method.
                    For usage info, type "python covld.py -h".

covld-dat.txt       Sample input file for covld.py.  The input format is
                    described in the header of this file.

This software is all in the public domain.

Alan R. Rogers

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covld's Issues

Can it handle missing data?

Can your code handle missing data (eg: a sample with no call at a loci)?
It isn't in the example and I don't notice it anyplace obvious in the code.
If the answer is "no", then that is a pretty bit limitation.

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