Entering edit mode
8.3 years ago
dirranrak
▴
20
Hi everyone,
Can anyone find what is wrong in these tped and tfam files? When I recoded them, I have got only one individual in map file that supposed to have many individuals.
tped file:
1 rs950122 0 836727 A B 0 0 A B A B A B A B A B
1 rs10492936 0 2926730 B B B B B B B B B B B B 0 0
1 rs10489589 0 2941104 B B B B B B B B B B B B B B
tfam file:
Yoruba YRI-NA18504 0 0 0 9
Yoruba YRI-NA18505 0 0 0 9
Yoruba YRI-NA18507 0 0 0 9
Thank you in advance
Can you post the .log file for your run?
My guess is that the .tfam file contains nonstandard linebreaks, and plink sees only a single line as a consequence. (If you type
xxd Genotypes_All.tfam | head
, what do you get?)If this is the case, your problem should go away after you standardize the linebreaks in the .tfam file.
I did what you are asking with plink and I got this. I don't really know what does it mean
That confirms that the linebreak bytes are the problem. They're supposed to be "0a" on OS X, not "0d".
You can fix this with:
Your conversion command should then work (and once you've verified that it works, you can delete
Genotypes_All_Old.tfam
).Great, thank you very much, it worked. But I want to know 1.where is my mistake in these steps? 2. How does this script really work? the
tr
,\r
and\n
.the original data is from Pan-Asian SNP Consortium web site which is like this
In the TextWrangler document options, you need to specify "Unix" instead of "Mac" line endings. (OS X actually does not use "Mac" line endings; that option only applies to much older Mac operating systems.)
Thank you again chrchang523.
My project is to find the origin of the population of Madagascar. So I need to compare the data from this country with those from Jewish, Arabic, Austronesian and African sub-Saharan. I have HGDP data but the first is a text file from Stanford University web site which is very big (~2 Go) and not in plink version and the another one is from Rosenberg lab web site which is a structure file.
I was looking for the way to convert these kind of file to plink file but the only one I found did not work. Help.