Clumping of multiple summary stats simultaneously

[asma.no...@gmail.com]

I am trying to perform LD clumping on multiple GWAS summary stats simultaneously using plink 1.9  as follows: 

plink --bfile 1000GP --clump file1.txt,file2.txt, ....,fileN.txt 

I got this error: Error: No variant ID field found in file1.txt. The head of this file is presented as follows:

chromosome position ID EA NEA eaf beta se p-value n_studies n_samples

1 13327 rs144762171 C G 0.036109 0.028899 0.049283 0.563183 7 13316

1 13980 rs151276478 C T 0.021873 0.094246 0.053583 0.082886 9 17201

1 30923 rs140337953 T G 0.733056 0.007243 0.024061 0.766603 6 10794

1 51479 rs116400033 A T 0.224105 -0.030820 0.022118 0.169466 8 12475

1 54490 rs141149254 A G 0.175406 -0.027056 0.020945 0.202769 9 17180

I don't understand why this error occurs ? Thank you for your help in advance

[Clement Isibor]

I am very much interested in the response to this challenge. 

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With kind regards 

Clement  N.Isibor  FMLSCN, PhD
Sent from Gmail Mobile

[Jean-Tristan Brandenburg]

Hi,

should you fine not respect head od summary statistics output from PLINK?

SNP and P?

otherwise, you can change with option :

--clump-snp-field <n...>  : Set --clump variant ID field name (default
                            'SNP').  With multiple field names, earlier names
                            take precedence over later ones.
--clump-field <name...>   : Set --clump p-value field name (default 'P').

best wish

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[asma.no...@gmail.com]

Hi, 

Thank you for your help. Indeed, this error occurs because of the column names of the summary statistics files.

I change the head in the files as it is required by Plink and the problem is resolved. 

I have another question, just to make sure that I understand correctly the output .clumped file generated by Plink (head and first row presented as follows): 

CHR    F                   SNP         BP        P    TOTAL   NSIG    S05    S01   S001  S0001    SP2

  11    7              rs174547   61570783  7.52e-217     2974   1099    298    289    291    997 rs2269928(7),rs2269928(8),rs2269928(9),rs2269928(10),rs2269928(13),rs2269928(14),rs2269928(17),rs2269928(101),rs2269928(109

Is SP2 field contains the clumped variants with the SNP rs174547 for all clumped summary statistics files given in input ?

Thank you again.

Best wishes, 

Asma

[Christopher Chang]

https://www.cog-genomics.org/plink/1.9/formats#clumped