feat: add benchmarking for fine-mapping using Alzheimer as example

[addramir]

✨ Context

This PR presents an example of fine-mapping of the GWAS catalog study for Alzheimer's disease (link to study). The study itself is a good benchmarking example for fine-mapping - relatively large number of SNPs, very strong signal on the 19th chromosome (APOE). It's worth noting that usually very strong signals are excluded from fine-mapping due to instability.

🛠 What does this PR implement

Summary:

• 10607272 SNPs in GWAS
• 33 clumps (32 without MHC)
• Fine-maping of all 32 clumps (without MHC) on my local machine using one cpu and a 2Mb window: 95 min (~3 min per locus). This run was performed without carma and sumstat imputation.
• The average number of overlapping SNPs between GWAS and LD was 6653.3125 SNPs.
• The complete fine mapping run of the APOE locus using carma and sumstat imputation took 19 minutes. It detected 152 outliers and imputed 715 SNPs.
• MHC fine-mapping run on 1MB took 9.5 min with 13188 SNPs in overlap.

🙈 Missing

🚦 Before submitting

• Do these changes cover one single feature (one change at a time)?
• Did you read the contributor guideline?
• Did you make sure to update the documentation with your changes?
• Did you make sure there is no commented out code in this PR?
• Did you follow conventional commits standards in PR title and commit messages?
• Did you make sure the branch is up-to-date with the dev branch?
• Did you write any new necessary tests?
• Did you make sure the changes pass local tests (make test)?
• Did you make sure the changes pass pre-commit rules (e.g poetry run pre-commit run --all-files)?

[addramir]

@Daniel-Considine Please have a look at this notebook. I run the fine mapping loop (no paralisation) on Alzheimer's disease and it seems to be a good toy example to benchmark your paralisation. Try running clumping and FM of your paralisation function on it (and I advise you to remove the MHC locus, see the notebook for details).

[Daniel-Considine]

@Daniel-Considine Please have a look at this notebook. I run the fine mapping loop (no paralisation) on Alzheimer's disease and it seems to be a good toy example to benchmark your paralisation. Try running clumping and FM of your paralisation function on it (and I advise you to remove the MHC locus, see the notebook for details).

Thanks Yakov, will take a look