remove variants with "." IDs

[Georg Otto]

Hi,

I have data in bed file format and would like to remove all variants with missing ID or ID "." using plink2. Neither --exclude-snp . nor --exclude-snps . seem to work.

Thanks a lot!

Georg

[Chris Chang]

Please post full .log file(s) when asking for troubleshooting help.

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[zorngibel]

sorry for that here is the log:

PLINK v2.00a5.2LM 64-bit Intel (11 Oct 2023)
Options in effect:
  --exclude-snp .
  --make-bed
  --out test/affymetrix.chr22.1kg.1
  --vcf imputed-1kg/affymetrix/vcf/affymetrix.chr22.vcf.gz

Hostname: login-a
Working directory: /rds/general/project/airwave/live/imputed_orig_merged
Start time: Thu Jun 27 19:55:38 2024

Random number seed: 1719514538
1031883 MiB RAM detected, ~873451 available; reserving 515941 MiB for main
workspace.
Using up to 256 threads (change this with --threads).
--vcf: 652226 variants scanned.
--vcf: test/affymetrix.chr22.1kg.1-temporary.pgen +
test/affymetrix.chr22.1kg.1-temporary.pvar.zst +
test/affymetrix.chr22.1kg.1-temporary.psam written.
3907 samples (0 females, 0 males, 3907 ambiguous; 3907 founders) loaded from
test/affymetrix.chr22.1kg.1-temporary.psam.
652226 variants loaded from test/affymetrix.chr22.1kg.1-temporary.pvar.zst.
Note: No phenotype data present.
Error: --exclude-snp variant '.' not found.

End time: Thu Jun 27 19:56:17 2024

[Chris Chang]

Please show that there is actually a variant named '.' in that file.