PLINK: Whole genome data analysis toolset [an error occurred while processing this directive]
Miscellaneous & TODO
Development of PLINK is ongoing: as such, there is always likely to be a list of features, listed here, that are only partialy implemented.

Matrix of pairwise LD (genotype correlation)

Correlations based on genotype allele counts (i.e. w/out phasing)

./plink --file mydata --r

./plink --file mydata --r2

These both create a file called 
	plink.ld
with the matrix of r or r^2 values in it.

TODO IBS sharing association tests

These tests are currently being implemented and are not ready for general use. 
	./plink --file mydata --sharing

TODO

Allow specific chromosomes and marker ranges only to be tested in the association analyses.

TODO

Implement haplotype-based test that fractionally counts all possible haplotypes.

TODO

Filters on Mendel rates, HWD, etc

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