User Tools

Site Tools


genetica:bgscheme_all

Procedure for 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
TWO_MARKER 1
PRINTTOP 50000
TEST <Test>
COMBIFILE <Pairs>  // if file is in working dir, else put path
COMBILIST 1
OUTPUTNAME <Output>
END
genetica/bgscheme_all.txt · Last modified: 2020/08/04 10:58 (external edit)