Plink 1.9 LD clumping without missing warning

[shihch...@gmail.com]

Dear Chris, 

Usually, we will receive some missing warning when the SNPs of the LD clumping is not existed in the main dataset like below. However, today, I find one situation, these two SNPs are missed in the main reference indivdiual genotype dataset, however, I didn't receive any missing warnings from the log file. Do you have any comments here? 

Thanks. 

Shicheng

Here is two input SNPs. 

SNP P
chr10_17129266_G_C 2.53915e-06
chr10_17131850_C_T 2.93985e-06

```

Warning: 'chr10_17178528_T_A' is missing from the main dataset, and is a top
variant.
Warning: 'chr10_17201444_G_GCCGCCCCACAGTGT' is missing from the main dataset,
and is a top variant.
Warning: 'chr10_17178610_C_G' is missing from the main dataset, and is a top
variant.
Warning: 'chr10_17202874_G_GCCTTTCCCTT' is missing from the main dataset, and
is a top variant.
Warning: 'chr10_17206202_T_A' is missing from the main dataset, and is a top
variant.
Warning: 'chr10_17206204_T_A' is missing from the main dataset, and is a top
variant.
Warning: 'chr10_17206206_T_A' is missing from the main dataset, and is a top

```

Here is log file:

PLINK v1.90p 64-bit (19 Feb 2020)
Options in effect:
  --bfile /home/sguo2/janssen4/db/UKB_QCed_WGS_GTEx/ukb23196_dedup_chr10
  --clump Pancreas.v8.signif_variant_gene_pairs.txt.extract.clumpin
  --clump-field P
  --clump-kb 500
  --clump-p1 1.0e-5
  --clump-p2 0.001
  --clump-r2 0.40
  --clump-snp-field SNP
  --make-bed
  --out Pancreas.v8.signif_variant_gene_pairs.txt.extract.clumpin
  --threads 12

Hostname: login01
Working directory: /expanse/projects/janssen4/dsci-csb/user/sguo2/baklava/clumping/WGS/CUBN
Start time: Wed Jan  5 14:12:54 2022

Random number seed: 1641420774
128131 MB RAM detected; reserving 64065 MB for main workspace.
187654 variants loaded from .bim file.
141948 people (0 males, 0 females, 141948 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
Pancreas.v8.signif_variant_gene_pairs.txt.extract.clumpin.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 141948 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.975412.
187654 variants and 141948 people pass filters and QC.
Note: No phenotypes present.
--make-bed to Pancreas.v8.signif_variant_gene_pairs.txt.extract.clumpin.bed +
Pancreas.v8.signif_variant_gene_pairs.txt.extract.clumpin.bim +
Pancreas.v8.signif_variant_gene_pairs.txt.extract.clumpin.fam ... done.
Warning: No significant --clump results.  Skipping.

End time: Wed Jan  5 14:13:16 2022