Process data from Hapmap for using LD Select method

HapMap-LDSelect-Processor: Use "LD Select" method (Carlson et al. 2004) to process HapMap genotype dump format data. Create lists of tSNPs, SNPs within haplotype blocks, and regions defined by SNPs. User's own genotype data and marker data can be analyzed too.

"LD Select" original code can be accessed at University of Washington, Nickerson's group Its v1.0 code was modified and used here so that it can process data from HapMap, and produce output conform to our format standard.

To prepare input for this program from HapMap dump: register and login http://www.hapmap.org, go to graphic browser, define the interesting region, then, download the "Dump SNP genotype data".

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

Warning: data of more than 1000 SNPs might have problem running for the moment.

Input:

1. Genotype data (check the corresponding option box to specify data type)

Please give the "Dump SNP Genotype data" from HapMap or from SIMP Genotype Query.

(if data from SIMP genotype query, )

Or use user's own data:

Please give the user's own genotype data in prettybase format (with four fields on each line, tab-delimited format: <Site Position><Sample ID><Allele 1><Allele 2>), be sure to use only unrelated individuals
Please give the user's own marker list in specified format (tab-delimited,with three fields on each line <position> <id> <chromosome>)

2. Filters:

r^2 filter to be used for LD Select
Minor Allele Frequency filter for LD Select

3. Optional outputs:

PrettyBase file (can be used in VG2 for visual display of "visual genotypes")
Original output from LD Select (description can be found at http://droog.gs.washington.edu/ldSelect.html)
htSNP lists and haplotype blocks defined by LD Select

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,