How to find top-hit SNP from gwas.

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2.2 years ago

Jalil Sharif ▴ 80

Hi,

I have downloaded a GWAS from IEU OpenGWAS. It has 17million+ SNPs, I want to find the 10 top hits, how can i do that?

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SNP GWAS tophits • 826 views

ADD COMMENT • link 2.2 years ago by Jalil Sharif ▴ 80

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What do you mean by a "hit"? "Top hits" usually refer to the result of a statistical test. Assuming that, what test do you have in mind?

ADD REPLY • link 2.2 years ago by ning ▴ 120

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Please send the format of the first few lines of the file you downloaded

ADD REPLY • link 2.2 years ago by LauferVA 4.2k

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The layout is as follows:

          SNP CHR     BP A1 A2   INFO    BETA     SE        LP    FRQ     N N_CAS         ID         P
1: rs12025928   1 546697  A  G 0.9244 -0.0212 0.1160 0.0679323 0.9244  2137  1169 rs12025928 0.8552000
2:  rs2977670   1 723891  G  C 0.9556 -0.0139 0.0926 0.0552213 0.9556 12776  7417  rs2977670 0.8806000
3:  rs3095826   1 770918  T  G 0.9953 -0.3052 0.5035 0.2640820 0.9953  3344  1678  rs3095826 0.5443999
4:  rs2905037   1 775426  G  A 0.9967 -0.0593 0.4184 0.0519295 0.9967  9522  5344  rs2905037 0.8873000

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ADD REPLY • link 2.2 years ago by Jalil Sharif ▴ 80

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