Tools/Softwares to find proxies for Indels
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When you find one, let me know :)
What I have done so far. Create a SNP-like format for your Indel/CNV add to your your SNP plink file and caculate D' or r2.
For instance
Instead Del/Del Del/x x/x use 11 12 22.
More detailed description:
http://bioinformatics.bc.edu/~marth/Download/SnpChipBasedDetection/McCarroll-CommonDelPol-NG-2006.pdf