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Procedure 4 all tests
SNP data set: 1000 Genomes Pilot 1
r2 threshold: 0.7
Population panel: CEU
Distance limit: 100
We substitute every marker for all its proxies and construct every possible pair for each file
Then, for every database, we choose the pairs which contains both makers in database. Aparently interSNP do this but it is very slow. We make this with a simple perl script. (download below)
Now we run intersnp with the obtained pairs and each database. Here we run all those test using a template for the selection file and writing the tags as needed.
BFILE <Database> // put path and name of plink bfile there
COMBIFILE <Pairs> // if file is in working dir, else put path