Clumping without rsID. Error: No variant ID field found in text file

[Davide Piffer]

I am trying to perform LD clumping on GWAS summary file. The problem is that the file lacks rsID and only has Chr and Pos columns. Hence I create a column named ID which is in the format #:Pos. I also run this command on the 1KG bed file:

./plink2 --bfile ~/genetics_2020/1kgtot_filt --set-all-var-ids @_# --make-bed --out ~/genetics_2020/1kgtot_filt.noid

So in both the 1kg bim file and in the gwas text file, the chr_pos column has this format: 1_10177

But when I try 

./plink --bfile ~/genetics_2020/1kgtot_filt.noid --clump-r2 0.1 --clump-kb 250 --clump-field p -clump-p1  0.00000005 --clump ~/Documents/schizophrenia/PGCALZ2sumstatsExcluding23andMe.new.txt --out ~/Documents/schizophrenia/ALZA.r2.5e8

I get Error: No variant ID field found in

/home/davide/Documents/schizophrenia/PGCALZ2sumstatsExcluding23andMe.new.txt.

I tried running the code with the  --clump-snp-field ID flag but I get the same error message.

How do I clump without rsID? Is it possible to do it using the position only?

[Christopher Chang]

Please post the full .log file from the failed --clump-snp-field run, and the first line of the --clump file.

[Chris Chang]

You'll need to preprocess the --clump file to replace commas with tabs/spaces; PLINK 1.x --clump does not accept CSVs.

On Thu, Feb 9, 2023 at 11:25 AM Davide Piffer <piffer...@gmail.com> wrote:

Here you go:

chr,PosGRCh37,testedAllele,otherAllele,z,p,N,ID
1,13668,A,G,-0.337420411213705,0.7358,74004,1_13668

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[Davide Piffer]

Thanks, it worked!