Use of 1000 genomes reference file

[Emily Morbey]

Dear GenomicSEM support team,

I just wondered if there is a specific reason for use of the 1000 genomes reference panel for the sumstats function. When I read in this file there are only ~9 million SNPs, so when I run this function I lose a lot of SNPs at the merge stage. 

Would it be fine for me to use a reference file with more variants? Or is there a reason I should stick with the 1KG reference?

Best wishes,

Emily

[Elliot Tucker-Drob]

sure. you can certainly use a different reference file as long as it is formatted the same way and has the same information. for rarer variants in particular, you would probably benefit from using in-sample LD, if available.

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[Emily Morbey]

Thank you. I would also like to check the naming conventions in the uploaded 1000G reference file. Does A1 refer to the ALT and A2 the REF? 

Emily

[agro...@gmail.com]

The reverse: 

A1 = REF

A2 = ALT