Converting map & ped files to binary file. Missing info

Question

[mulderharko]

Hi

I'm having trouble converting map and ped files to binary files. I get the following error message.

plink --allow-extra-chr -chr-set 18 \
  --chr 1-18 \
  --file TestRow \
  --make-bed \
  --out TestRowBinary
PLINK v1.9.0-b.7.7 64-bit (22 Oct 2024)            cog-genomics.org/plink/1.9/
(C) 2005-2024 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to TestRowBinary.log.
Options in effect:
  --allow-extra-chr
  --chr 1-18
  --chr-set 18
  --file TestRow
  --make-bed
  --out TestRowBinary

15983 MB RAM detected; reserving 7991 MB for main workspace.

Error: Line 189 of .map file has fewer tokens than expected.

Looking at the map file the base pair position for the particular SNP's seems to be missing:

Line 188  2 2_133796709 0 128552942
Line 189  2_138069646 0 
Line 190  2 2_138926958 0 133606416

Not analyzing the SNPs with missing information is not a huge loss, but I'm unable to proceed with this error. I notice there are several more SNPs with a similar problem.

Is there a way to filter out these SNPs from the map & ped files to be able to proceed to the binary file?

Thanks