Sunday, September 18, 2011

Do-It-Yourself Dodecad v 2.1

DIYDodecad v 2.1 allows incomplete genotype files to be used, i.e., genotype
files that do not include all expected SNP markers used in a calculator. This
is useful to individuals having older genotype files from their testing
companies, and allows the tool to be used with any type of genotype data, and
not only the Illumina platforms currently used by 23andMe and FamilyTreeDNA.

There is a minimum requirement of at least 100 usable SNPs, i.e., SNPs that are
in the genotype file and do not have no-calls.

If you had previously followed the instructions carefully, and got an "end of file reached" error, this was most likely due to your genotype file lacking some of the expected markers used in the calculator. Version 2.1 should work for you.

You can download it from here (Google Docs, File->Download Original), or here (Sendspace). Uncompress DIYDodecad2.1.rar to a local directory on your computer, and follow the instructions in the README.txt file.

Past versions: 2.0, 1.0

17 comments:

  1. I tried to download the Windows executable file using IE6 & Firefox and got a 404 file not found error message. The README.TXT came down OK. Also there is no DIYDodecad2.1.rar file on the GoogleDocs link??

    ReplyDelete
  2. See post:

    File->Download Original

    ReplyDelete
  3. I've downloaded everything however I keep getting this error, the genotype.txt permission denied?

    My file name:

    standardize('wali.csv', company='ftdna')

    Error message:

    Error in file(file, ifelse(append, "a", "w")) :
    cannot open the connection
    In addition: Warning message:
    In file(file, ifelse(append, "a", "w")) :
    cannot open file 'genotype.txt': Permission denied

    ReplyDelete
  4. When you run


    standardize('wali.csv', company='ftdna')


    in R, make sure that you are in the same directory as the one in which DIYDodecad resides.

    Also, make sure that wali.csv has indeed been unzipped, because it might appear as wali.csv in Windows, if in reality it is still wali.csv.gz, if your settings are to hide file extensions.

    ReplyDelete
  5. what is the run command for MacOs?

    ReplyDelete
  6. Replies
    1. I was able to run DIYDodecadWin.exe under MacOS using Wine:
      /Applications/Wine.app/Contents/MacOS/startwine DIYDodecadWin.exe dv3.par

      Delete
  7. I am getting the same error message as the first reply: "I tried to download the Windows executable file using IE6 & Firefox and got a 404 file not found error message". Any suggestions?

    Thank you

    ReplyDelete
    Replies
    1. I have got the same problem, please do someone know the solution?

      Delete
  8. I am having a problem getting of the ground.
    I have downloaded R and installed it and have opened Dodecad and placed it in a folder in my C drive under windows XP.
    R is in C:/Programme files/R/R-2.13.1
    Dodecad is in C:/diydodecode/twopointone/ and includes standardize.r

    When I open R and put in setwd('/C/diydodecode/twopointone’) enter I get
    > setwd('/C/diydodecode/twopointone’)
    +
    which I don't think is correct because if I then add at the cursor after the + source('standardize.r')and enter

    > setwd('/C/diydodecode/twopointone’)
    + source('standardize.r')

    I get
    > setwd('/C/diydodecode/twopointone’)
    + source('standardize.r')
    Error: unexpected symbol in:
    "setwd('/C/diydodecode/twopointone’)
    source('standardize.r"
    >

    The other alternatives I have used to setwd are
    setwd('C:/diydodecode/twopointone’)
    setwd('/diydodecode/twopointone’)
    setwd('c/diydodecode/twopointone’)
    setwd('/c:/diydodecode/twopointone’)
    all with the same result

    I am obviously doing something wrong but I can't see it.

    thanks
    Bob

    ReplyDelete
  9. setwd('/C/diydodecode/twopointone’)

    You used ' to open the quote and ’ to close it. So, R thinks that the quote hasn't closed yet, and expects more input, hence it gives you the + sign.

    Follow the instructions to the letter, and it will all work out.

    ReplyDelete
  10. Thanks
    It had to be a little, but big, error like that.
    Bob

    ReplyDelete
  11. I have a problem with Mac Os X but I want to check my data (23andme)
    Please make EuroCal and this program Web based so everybody could use those programs by temporary uploading raw data and checking. Raw data will be automatically deleted (or not deleted, it is up to you or user) later on
    Thank You it is great program Dodecad v3

    ReplyDelete
  12. I have a 23andme test kit on the way. Can I still use this version to find deep ancestry respective to population groups? ex. Atlanto-Baltic, Mediterranean? Thanks

    ReplyDelete
  13. Hi,

    I have raw 23andMe Data, I went through R and standardized the genotype.txt, and when I go and open up DIYDodecad dv3.par in the Windows Command prompt, I get two things: "166,642 SNPs Absent", out of 166,642 total SNPs and I get "Fewer than 100 useable SNPs"

    I am so confused -- and on many various things regarding my DNA results.

    ReplyDelete
  14. Greetings,

    Thank you for creating this wonderful site. It is very enjoyable and informative.

    I have a a raw data file recently released by AncestryDNA. The layout is similar, but there are differences between 23andMe and A-DNA. I did a test standardization run that produced results much different from A-DNA in DV3 and K12b, but DV3 and K12b are consistent with census data, newspaper articles, and family lore.

    Do you think the standardizing process is compatible with Ancestry's raw data? I have the results below.

    Thank you so much!

    Ancestry
    British Isles 59%
    C European 21%
    Finnish/Volga-Ural 11%
    Scandinavian 7%
    Uncertain 2%


    DIYDodecad DV3
    166462 total SNPs
    0 flipped SNPs
    164808 heterozygous
    0 no calls
    1654 absent SNPs
    0.990064 genotype rate mode genomewide
    6.15% East_European
    18.80% West_European
    8.37% Mediterranean
    20.12% Neo_African
    3.03% West_Asian
    4.75% South_Asian
    4.25% Northeast_Asian
    9.24% Southeast_Asian
    7.24% East_African
    0.20% Southwest_Asian
    1.53% Northwest_African
    16.33% Palaeo_African

    K12b
    6.29% Gedrosia
    2.08% Siberian
    0.93% Northwest_African
    4.70% Southeast_Asian
    12.78% Atlantic_Med
    13.32% North_European
    3.99% South_Asian
    12.16% East_African
    1.26% Southwest_Asian
    5.72% East_Asian
    4.50% Caucasus
    32.27% Sub_Saharan

    ReplyDelete
  15. I'm also having trouble getting off the ground. I think I successfully changed the working directory, but when I enter source('standardize.r') I get:
    Error in file(filename, "r", encoding = encoding) :
    cannot open the connection
    In addition: Warning message:
    In file(filename, "r", encoding = encoding) :
    cannot open file 'standardize.r': No such file or directory

    And then from there I'm thoroughly confused. Sorry, programs with command input aren't my forte!

    ReplyDelete