Generate your own simulated data

  1. Use SeqSIMLA to get simulated data (.ped, .map...).
  2. Download .legend file from 1000G.
  3. Download parse.pl.
  4. Put your SeqSIMLA data, .legend file and parse.pl in same folder.
  5. Execute parse.pl with below parameters, and you will get .bed, .bim, .fam and a new .legend.

    --ref file_name: the name of .legend file.
    --map file_name: the name of .map file.
    --ped file_name: the name of .ped file.
    --ref_out file_name: the name of new .legend file (Optional).
    --ref_pos line_number: which line you want to start to replace snps's name and snp's position from .legend to your .map (Optional).
    Note: if --ref_pos is not in the command, parse.pl will choose a line randomly.

    For example,
    perl parse.pl --ref ALL_1000G_phase1interim_jun2011_chr1_impute --map test --ped test --ref_out chr1 --ref_pos 10000
  6. Get annotation file:
    1. Upload the new legend file to SeattleSeq website
    2. Choose "custom" for input file format and also fill out all information about your input file.
    3. Click "Submit".
    4. You will receive a download link email from SeattleSeq after your annotation file is ready to download.
  7. After you have done all steps, you will get .bed, .bim, .fam and a annotation file.
Enjoy your work with FamPipe :)