HapMap-Haploview-Processor: Process haplotype blocks and tSNPs data produced by HapMap Project

Three different algorithms implemented in Haploview for constructing haplotype blocks and selecting htSNPs: Gabriel's method, Four Gamete Rule, and Solid Spine of LD.

Extracts SNP list data from Hapmap data and Haploview exports.  The output data includes tSNPs list, SNPs within & outside of haplotype blocks, regions covered by haplotype blocks,

To prepare input for this program by the following steps,

  1. Register and login http://www.hapmap.org, go to graphic browser, define the interesting region, then, download the "Dump SNP genotype data".
  2. Load the "Dump data" into haploview, in "Check Markers" tab, "Export current tab to text", save into one file; in "Haplotypes" tab,  "Export current tab to text" and save into another file.  Both files will be used in this program.

Warning: need to use data produced by v2.05 Haploview. Early version would not work. Also, hapmap dump has duplicated entries.

Perlegen genotype data obtained from SIMP Genotype Query can be used here too.

Input:  

1. Please give the "Haplotypes" tab data from Haploview. (format example)

2. Please give the "Select Markers" tab data from Haploview. (format example)

3. Please give the "Dump SNP Genotype data" from HapMap. (format example)

4. Please specify the email address where the results can be delivered:

Email address  

5. Output in gzip compressed format:

Your email box accepts message size limit of  per message

If your input data file is from a Mac machine, please be sure to check this box

 

Authors: Chunyu Liu,