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Haplotype Block Detection

8.3 Haplotype Block Detection

When studying haplotypes in the human genome, it is often desirable to try and define the location of haplotype blocks: ‘sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed’ [Gabriel 2002].

With the Haplotype Block Detection dialog, you have the ability to detect haplotype blocks in your SNP data using the method described in defining paper by Gabriel et al. [Gabriel 2002].

Block Detection Options

In the Block Definition Algorithm group of options, you can set parameters to control the ‘Gabriel et al.’ algorithm. The defaults specified are the ones found in the paper suggested from empirical results and biological intuition.

You can also specify in the General Options a MAF threshold under which markers are ignored in the context of the algorithm. The maximum number of markers in a block and maximum length of a block in kilo-base pairs defines upper bounds of a block’s size using two different metrics for size.

Haplotype Estimation Options

Like in Haplotype Association Tests, you can select the haplotype estimation method and the options that define it’s behavior for estimating haplotype frequencies.

For block detection, the frequencies are used to computed D′ statistics and one-sided confidence bounds for the D′.

See How Haplotype Frequencies are Computed for more details.