Jonathon LeFaive
Jonathon LeFaive
Your input target genotypes have the alleles switched when comparing against all 3 reference panels (see below). I'm guessing that v4.0.3 is allowing for this (maybe intentionally) (@Santy-8128 might be...
This is already fixed in the master branch of libStatGen. You can download at https://github.com/statgen/libStatGen/archive/master.zip.
bamUtil is looking for libStatGen in the location "../libStatGen" relative to the bamUtil folder. You unzipped master.zip in the bamUtil directory instead in the parent directory. Also, master.zip unzips into...
You are probably using a compiler that doesn't fully support c++11 (e.g., gcc v4.8). Can you run `c++ --version` to confirm this?
Try adding `include_directories(${ZLIB_INCLUDE_DIR})` to line 14 of CMakeLists.txt (https://github.com/statgen/METAL/blob/master/CMakeLists.txt#L14).
The install.sh script should no longer be used (should have been deleted). Instead follow the instructions in the README to build from source. You will likely need to use a...
`sav merge` existed in version 1.x because the first version of the file format only allowed for bi-allelics and limited FORMAT fields. The second version of the SAV file format...
Maybe try setting the region to 21:1-48129895. I don't think multiple chromosomes in a single file has been tested.
If that doesn't work, try compressing chromosome 21 as a separate file and removing the --region option. Let me know how it goes so that I can make multiple chromosome...
How was the tbi index generated? Can you share the tbi file?