How does GenomicSEM merge summary statistics with LD-score files?

[Thanh Le]

In the ldsc() step, I lost about 36k SNPs after merging with LD-score files. I'm guessing that it could be due to the difference in SNP, CHR, or BP, but I'm not sure how the other columns in LD-score files are used.

Could you explain how GenomicSEM merge the summary statistics with LD-scores files?

Thanks.

Best,

Thanh Le

[Michel Nivard]

Could you share the full log? ITs not uncommon for SNPs to be in one file, but no0t the other, and there is also some processing happening.

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