What is minRatio option?

Open chulghim opened this issue 4 years ago • 1 comments

I got this message: Chunk 3 has less than 0.1% of variants from the GWAS panel overlapping with the reference panel ... Please increase the value of "--chunkSize" to analyze larger chunks or decrease the value of "--minRatio" = 0.1

Afte that, i decreased the value of --minRatio and then, it worked good. and ChunkSize doen't work.

I want to know the meaing of minRatio.

Mar 03 '21 00:03 chulghim

This message is referring to the Sites(GWAS/Ref/%) column in the log. If there aren't enough sites in your array data (labeled GWAS) compared to the reference panel (labeled Ref), then the accuracy of your imputation results may suffer. Increasing --chunkSize will only help if the current --chunkSize is too small and some of the chunks are entirely made up of sparse regions in your array data.

Mar 03 '21 14:03 jonathonl