This folder contains the tools used for making the sqLite database contained in
this package from the raw PolyPhen files.

Homepage for PolyPhen :

  http://genetics.bwh.harvard.edu/pph2/ 

Making the sqLite database :

  1. Download polyphen2_dbsnp131_2010-07-05.tar.gz from

       http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/

  2. Uncompress the downloaded files.
     These uncompressed files are the "source files" located here :

       ~/PolyPhenForge/srcdata/PolyPhen.Hsapiens.dbSNP.20100705/downloads

     NB: The PolyPhen output format is described in these files :

      README 
      pph2_output_format.pdf 

  3. Three text files were used to forge the database :
      pph2_snp131_missense_HumVar-short.txt
      pph2_snp131_missense_HumDiv-full.txt
      snp131_duplicate_rsids.txt 

  4. Adjust settings in createPolyPhenDb.R and run it.

