АвторТема: Eurogenes fastIBD.  (Прочитано 4137 раз)

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Eurogenes fastIBD.
« : 20 Август 2013, 23:52:19 »
Hello fellow DNA enthusiast,
David over at Eurogenes have started running a fastIBD run, but for now he has released only a teaser,
its a good way for us as a community to get our heads working on how to easiest represent and get the most out of the data supplied.
Last time Eurogenes released a fastIBD analysis,
a Canadian DNA cousin of mine created a easily readable office type file,
that gave people many advantages in interpreting the data without holding a Phd in Office tools, and i am hoping he will come to our rescue this time around too :)

Anyways, here: ( https://www.dropbox.com/s/2px46mrf07ovg4l/Chr1.zip ) is the new fastIBD file for chr 1, the rest will be released in the not to distant future if everything goes well.

Some basic instructions:

Looking at the Main file for the matches, we see the matches in this fashion:

Orcadian_HG00118_a   Norwegian_NO1_a   12855   13032   8.92E-012

If i remember correctly the E number indicates reliability level, while the number infront of the E indicates cM size and the other numbers the range of shared SNP's. Thus the match between the Orcadian and myself is 8,92cM, 177 SNP's and a reliability of 012, which is fairly low on a range between 10-120.

Оффлайн evonАвтор темы

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Re: Eurogenes fastIBD.
« Ответ #1 : 21 Август 2013, 00:54:38 »
Also with regards to using R:
For more accurate results, please swap the sex averaged cM distances in the marker and bim files to male and female specific cM distances, which can be found in the 260K_SNP_cM text file. To do that, you need to change the marker and bim files to text files and swap the cM column in Excel. Or you can just use the sex averaged cM distances...

Of course, you'll need the latest R installed the run the ibd2segment script.

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Re: Eurogenes fastIBD.
« Ответ #2 : 21 Август 2013, 08:30:20 »
Thanks for the information.

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Re: Eurogenes fastIBD.
« Ответ #3 : 09 Сентябрь 2013, 00:39:25 »
As mentioned by evon,a  Google Group has been established for the dissemination and discussion of this new Eurogenes IBD run. You may recall that one was run about a year ago. This one is using build 37 bim files (as opposed to build 36) and has several hundred new participants. Furthermore, all the analysis is being done by David Weslowski, so you don't need to run R script to receive your results. If you are a Eurogenes participant and interested to see if you are in this current run ( a few participants have not been included in this run) send me a PM with your Eurogenes id number.


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