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.
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??
ReplyDeleteSee post:
ReplyDeleteFile->Download Original
I've downloaded everything however I keep getting this error, the genotype.txt permission denied?
ReplyDeleteMy 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
When you run
ReplyDeletestandardize('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.
what is the run command for MacOs?
ReplyDeleteMacOS is not supported.
ReplyDeleteI was able to run DIYDodecadWin.exe under MacOS using Wine:
Delete/Applications/Wine.app/Contents/MacOS/startwine DIYDodecadWin.exe dv3.par
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?
ReplyDeleteThank you
I have got the same problem, please do someone know the solution?
DeleteTry using chrome!
DeleteI am having a problem getting of the ground.
ReplyDeleteI 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
setwd('/C/diydodecode/twopointone’)
ReplyDeleteYou 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.
Thanks
ReplyDeleteIt had to be a little, but big, error like that.
Bob
I have a problem with Mac Os X but I want to check my data (23andme)
ReplyDeletePlease 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
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
ReplyDeleteHi,
ReplyDeleteI 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.
Greetings,
ReplyDeleteThank 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
I'm having the exact same issue! I used my AncestryDNA raw autosomal file and got results that were quite different from those of Ancestry.
DeleteAncestry: Dominantly Great Britain (35%) and Europe West (22%)
K12b: Dominantly Sub-Saharan (32.27%) and North European (13.32%)
And, typing this, I just noticed that datawise, Sonia Haga and I are identical, though our AncestryDNA data is different! Please assist us.
-----------------------------------------------------------
ReplyDelete-- DIY Dodecad v 2.1 --------------------------------------
------------------------------------------------@@@@@@@----
-- Copyright (c) 2011 Dienekes Pontikos -------@@-----@@---
------------------------------------------------------@@---
-- More information: ---------------------------@@@@@@@----
----- Dienekes' Anthropology Blog -------------@@----------
-------- http://dienekes.blogspot.com ---------@@----------
----- The Dodecad Ancestry Project ------------@@@@@@@@@---
-------- http://dodecad.blogspot.com ----------------------
-----------------------------------------------------------
12 ancestral populations
166462 total SNPs
At line 173 of file DIYDodecad.f90
Traceback: not available, compile with -ftrace=frame or -ftrace=full
Fortran runtime error: Bad value during integer read
Warning message:
running command 'DIYDodecadWin dv3.par' had status 2
What does this mean?
how do i get this program to analyze ancestrydna files? i tried but it kept crashing
ReplyDeleteI tried to downloaded it for mac but was not able to do so.
ReplyDeleteWhat are the steps for a Mac?
ReplyDelete