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statgen / METAL

Meta-analysis of genomewide association scans
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allele 1 vs. Effect allele in output file #35

Closed PyunJung-Min closed 1 year ago

PyunJung-Min commented 1 year ago

Hi, thanks for the wonderful tool.

I have a question about "allele 1" in the output file.

If I understood correctly, "allele 1 in the output file" is not always effect allele, but could be effect allele or non-effect allele. Is this right?

If I like to know only effect alleles and their frequency/se/p-value of the meta-analysis output file, how can I get it?

I would appreciate for any help!

Many thanks in advance.

Jung-Min Pyun

welchr commented 1 year ago

Allele frequencies and effect sizes are all oriented towards allele 1. This should be printed in the .info file that METAL produces.

https://github.com/statgen/METAL/blob/ab5d19155aa72cef5ca5d2876aea0dd6b9fcba0d/metal/Main.cpp#L729-L735