Jonathon LeFaive
Jonathon LeFaive
It looks like the libStatGen being linked was built with an older version of gcc (< 5). Is it possible that libStatGen is installed in a system path somewhere? Or...
Yes, you can clean the libStatGen directory by running `cd ../libStatGen && make clean`.
You can leave this open, I will look into the Mac issue when I get a chance.
The only difference that is known to affect results is the handling of multiallelic sites. Can you elaborate on doesn't make sense according to my data?
Ok. I'll test that exact command and get back to you. It might take a couple days to get to this though.
Can you pull the latest from the develop branch and give it a go? You will need to reinstall the savvy dependency as well after pulling the latest (`cget remove...
That is the correct commit id. A tarball can be found at https://github.com/statgen/EPACTS/archive/98d7ff7c0f0831d521324f16671d8fa989800f63.tar.gz. Are you saying that you are getting the same exact results when running b.glrt with this commit...
I did some tests with the Filtered.txt VCF file you supplied. One problem is that this file has carriage returns, which breaks the parsing on the master branch version (v3.30)....
Just needs a tar.gz at the end https://github.com/statgen/EPACTS/archive/98d7ff7c0f0831d521324f16671d8fa989800f63.tar.gz
The versions are admittedly a little wonky, and I will eventually clean that up. In the meantime, let me make some clarifications. According to recipe_3.3.0.txt, what you are calling v3.3.0...