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immunogenomics / HLA-TAPAS

HLA-TAPAS pipeline for HLA association and fine-mapping studies
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HLAassoc > Omnibus Test #18

Open DelnazRoshandel opened 2 years ago

DelnazRoshandel commented 2 years ago

I want to try omnibus test and I am wondering how the .bim file of reference panel should look like, should all the AA that are on the same position have the same coordinate? I did HLA imputation on Michigan server and there is a one base per difference between AAs that are on the same position:

6 AA-A--2-29910398-exon1-R 0 29910398 T A 6 AA-A--2-29910398-exon1-W 0 29910399 A T 6 AA-A--2-29910398-exon1-x 0 29910400 T A

And often the coordinate doesn't match the one that in is the ID:

6 AA-A--22-29910338-exon1-V 0 29910385 A T

DelnazRoshandel commented 2 years ago

Ok I find the link for the. bim files here: https://github.com/immunogenomics/HLA-TAPAS/issues/15

Which is similar to what I had. So I am assuming somehow it works.

Now I have other problems with omnibus test. First of all it doesn't recognize the "OMNIBUS_LINEAR" and says "invalid choice: 'OMNIBUS_LINEAR' (choose from 'LOGISTIC', 'LINEAR', 'OMNIBUS')"

And when I choose "OMNIBUS", I get another error:

Traceback (most recent call last): File "/python/3.8.0/lib/python3.8/runpy.py", line 192, in _run_module_as_main return _run_code(code, main_globals, None, File "/python/3.8.0/lib/python3.8/runpy.py", line 85, in _run_code exec(code, run_globals) File "/HLA-TAPAS/HLAassoc/main.py", line 227, in HLAassoc(args.Main_Menu, args.out, args.dependency, File "/HLA-TAPAS/HLAassoc/HLAassoc.py", line 446, in init if exists(which("Rscript")): File "/python/3.8.0/lib/python3.8/genericpath.py", line 19, in exists os.stat(path) TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

steletvinicius commented 9 months ago

Got the same error solved installing R on your virtual environment running HLA-TAPAS.