P value conversion during extracting lead variants
gwaslab<=3.4.18 : In older versions, gwaslab converts MLOG10P to P (if P column is not available) and then uses P to extract lead variants using .get_lead(). But during conversion, since MLOG10P was set as float32, and then P was accordingly set as float32. The minimum of float32 is around 1e-38, below which P values will become 0. This could cause error when extracting lead variants.
Solution: simply use scaled=True to directly use MLOG10P instead of P values.
Skipped lead variant in extracting lead variants
gwaslab<=3.4.22 : When extracting lead variants using .get_lead(), if the lead variant is the last variant in all significant variants, it will be mistakenly skipped.
Solution: Update to new version of gwaslab.
Regional plots : color issue
gwaslab<=3.4.39 : the color assigned to each variant is actually the color for the lower LD r2 category. For example, variants with LD>0.8 will be colored with the color for 0.8>LD>0.6.