Rare variant meta-analyzing tests

Question

[Floris Brenk]

Hi all,

I have 5 different (dosage VCF files, with both continuous and binary phenotypes) datasets and I'm trying to meta-analyze rare variants in each dataset. Ideally I would like to group the variants per gene and then meta-analyze the p-values per gene from all 5 datasets, but I haven't found any software that easily does that. I played around a bit with rare metal and rvtests, but so far I keep on running into errors and weird results. Does anyone has any tips, ideas or tricks how to best do this? Any help is really appreciated!

Answer 1

[swetansu]

Have you tried SKAT/SKATO? R package SKAT has the details!! Worth exploring custom weighing scheme besides default MAF based weighing..