--clump-snp-field flag error?

[Megan T]

Hi! In my base data file, the SNP IDs are under the column header "SNP" and p-values are under "PVAL". While doing LD-based result clumping, I denoted that these were the header names using --clump-snp-field and --clump-field flags. However, when I run plink, I get error. that there is no variant ID column found. Could I please get some help? Here's the log: 

PLINK v1.90b6.22 64-bit (16 Apr 2021)
Options in effect:
  --bfile pgx_mis20201208_cleaned20210219
  --clump PGC3_EUR_QC
  --clump-field PVAL
  --clump-kb 250
  --clump-p1 1
  --clump-p2 1
  --clump-r2 0.10
  --clump-snp-field ID
  --out IMPACTclumped2

Random number seed: 1720107958
48139 MB RAM detected; reserving 24069 MB for main workspace.
7521999 variants loaded from .bim file.
3378 people (1173 males, 2205 females) loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 3378 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.999998.
7521999 variants and 3378 people pass filters and QC.
Note: No phenotypes present.
Error: No variant ID field found in PGC3_EUR_QC

Thank you so much!

[Megan T]

Sorry, typo- the column name for the SNP IDs is "ID" (as in the log) and not "SNP"

[Christopher Chang]

What is the output of "head -n 2 PGC3_EUR_QC"?

[Megan T]

[Christopher Chang]

That wasn't the output of "head -n 2 PGC3_EUR_QC", and the difference is why your command didn't work.  --clump does not ignore "##" header lines.

[Megan T]

Got it, thanks so much! It works now