Thank you for sharing the tools you are using. I didn’t know many of the tools you mentioned here, and they look very useful! I am looking forward to trying them out next time! I also would like to share two tools I use after GWAS.
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LocusZoom: Makes Manhattan plots interactive and provides a qualitative assessment of QQ plots. +1 point for accepting summary stats without rsID, annotating them, and allowing users to download the file with rsID.
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FUMA: A one-stop screening solution for various enrichment analysis.
Regrading the additional analysis, I often conduct PRS analyses. I also like to conduct Mendelian randomization and LD score regressions, provided there is enough power.