GWAS summary statistics without all SNPs

SARA POLO ALONSO

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Feb 23, 2024, 3:57:47 AM2/23/24

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Hello,

I have run a job (ID: 452895), and the Manhattan plot of the Summary statistics of my GWAS lacks of many SNPs that were present in my initial GWAS. Captura de pantalla 2024-02-23 095638.png

Captura de pantalla 2024-02-23 095638.png

I have converted my sumstat from hg38 to hg19 with liftOver using the ucsc files. I would like to know the reason why this is happing so that I can solve the problem.

Thank you,

Sara

fuma.ctglab

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Feb 25, 2024, 8:27:11 AM2/25/24

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Dear Sara,

Unfortunately the description of your issue is a bit vague. Could you be a bit more specific about which snps you're missing? Then, we can try to look at what happen to these specific snps.

Also, the conversion from hg38 to hg19 are not going to be 100% perfect so it needs to be taken into account that sometimes liftover would fail to convert some snps.

Thank you,
FUMA

SARA POLO ALONSO

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Feb 26, 2024, 4:32:25 AM2/26/24

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Hi again,

I have checked the summary statistics and the problem has to do with the conversion form hg38 to hg19. It is now solved.

Thanks for your help,

Sara

El dia diumenge, 25 de febrer del 2024 a les 14:27:11 UTC+1, fuma.ctglab va escriure:

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