Need to convert your genotyping files into EIGENSTRAT format? Here is a quick primer to do so. If you haven't already, download the EIGENSTRAT package and extract the contents. We will be using the convertf tool to convert your genotypes to EIGENSTRAT format. The convertf tool can convert to/from ANCESTRYMAP, EIGENSTRAT, PED, PACKEDPED, and PACKEDANCESTRYMAP files.
First, check to see if your convertf program is working out of the box by going to the /bin directory and typing in ./convertf. Mine was not working (Error message:./convertf: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by ./convertf)). My quick fix was to try to recompile things based on the included C code, but going to the src directory and typing make convertf did not seem to do the trick. Skimming through the README file I saw that you can remake the entire package by again going to the src directory and typing make clobber and then make convertf (the recommended make install produced errors on my system). Typing ./convertf finally returned the "parameter p compulsory" output indicating the program is now working. (Note: make clobber will remake the entire package and likely require you to remake other packages you need to use, ex: make mergeit, make eigenstrat, etc.). I am not a UNIX guru, so if you know of a better way to get convertf running, please let me know in the comments.
Now that we have a running version of convertf, we can begin making a parameter file (ie: the par.PED.EIGENSTRAT file) for converting from one file format to another. The included README file in the CONVERTF directory is instrumental for doing this. Since .ped and .map files are ubiquitous, I will use this as an example to convert to EIGENSTRAT format. Below is a parameter file to do so, but again converting to/from other formats is possible as well.
Finally, save this file as par.PED.EIGENSTRAT and run it by simply going into the directory with your working convertf program (mine was in the /EIG5.0/src directory) and put in the command ./convertf -p dir/par.PED.EIGENSTRAT, where dir is the directory your par.PED.EIGENSTRAT file is saved in. You can essentially call the par.PED.EIGENSTRAT file any name, but this name meshes nicely with that in the samples that come with EIGENSTRAT. Hope this is helpful, feel free to comment with questions.
I still have no idea how to run this. Where do you save this parameter file? Do you name it par.PED.EIGENSTRAT? If not, how else does the command know where the parameter file is?
ReplyDeleteIn the above example you save the parameter file as par.PED.EIGENSTRAT, but you can call it whatever you want as long as you give the directory and filename of the correct parameter file after the convertf command in UNIX. I reworded things in the post to hopefully make things more clear. Let me know if it helps and thanks for checking out the site.
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ReplyDeleteI have bim/fam/bed files not ped and map. How can I make a parameter file with them?
ReplyDeleteThanks
You can use plink to first convert it to a ped/map format. Use plink --bfile yourfile --recode --out yourfilehttps://genometoolbox.blogspot.com/logout?d=https://www.blogger.com/logout-redirect.g?blogID%3D3215661876653517169%26postID%3D4574047875097522322
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