Defining fine-mapping regions

[dajana-panovic]

Hello,

Could you please give me some more details when it comes to defining regions for fine-mapping?
I was referring to instruction given here on the GitHub:

1. Preprocessing
   For each genome-wide significant locus (default configuration: P < 5e-8), we define a fine-mapping region by taking a 3 Mb window around a lead variant (and merge regions if they overlap). We preprocess an input GWAS summary statistics into separate files per region for the following steps.

2. LD computation
   We compute in-sample dosage LD using LDstore2 for each fine-mapping region.

3. Fine-mapping
   With the inputs of summary statistics and in-sample LD from the steps 1-2, we conduct fine-mapping using FINEMAP and SuSiE with the maximum number of causal variants in a locus L = 10.

However, recently I come up on this issue #36. As I understood MHC regions should be excluded? Why is that the case? Are there any other regions that we should exclude as well? Also, what is the usual value for max_region_width parameter that you used in you analysis?
Any additional advice or suggestion in this regard?

Also, could you tell me what is the biggest region that you managed to process with susieR and what was the number of samples included?

Thank you very much!
Best,
DPanovic