Detritus Wiki

• First we took the every provided file (listTEST5.txt, listTEST6.txt, listTEST15.txt, listTEST16.txt) and look for the proxies for every marker at http://www.broadinstitute.org/mpg/snap/ldsearch.php with,

    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
TWO_MARKER 1
PRINTTOP 50000
TEST <Test>
COMBIFILE <Pairs>  // if file is in working dir, else put path
COMBILIST 1
OUTPUTNAME <Output>
END

• Results and other files could be downloaded from https://docs.google.com/folder/d/0B8-42LJtMhdZSTVrZEZCU3d6NUE/edit