Missing variants after updating position

[Anna]

Hello, I want to update positions of markers in my dataset. Plink starts with 777962 variants and it updates all of them and then gives me only 760832 variants in the new file. Please see below the log file. Can someone explain what is happening? I don't specify any filters or QC, only updating the positions. Also, is there at least any possibility to see which markers were excluded? Thank you very much for any help!

PLINK v1.90b3.46 64-bit (13 Feb 2017)

Options in effect:
  --allow-no-sex
  --bfile data_380_sorted
  --chr-set 29
  --make-bed
  --out update_380_pos
  --update-map updatePos.txt

Start time: Wed Nov 18 14:38:14 2020

Random number seed: 1605706694
386705 MB RAM detected; reserving 193352 MB for main workspace.
777962 variants loaded from .bim file.
380 samples (0 males, 0 females, 380 ambiguous) loaded from .fam.
Ambiguous sex IDs written to  update_380_pos.nosex .
380 phenotype values loaded from .fam.
--update-map: 777962 values updated.
Warning: Base-pair positions are now unsorted!
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 380 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.
Total genotyping rate is 0.988483.
760832 variants and 380 samples pass filters and QC.
Among remaining phenotypes, 122 are cases and 258 are controls.
--make-bed to  update_380_pos.bed +  update_380_pos.bim +  update_380_pos.fam ... done.

End time: Wed Nov 18 14:38:16 2020

[Christopher Chang]

Hi, can you post or send me the .bim and --update-map files you used in this run (.bed and .fam should not be necessary), so I can reproduce what you're seeing?  Thanks.

[Anna]

Sure, thank you for helping! It says the bim file is too big to upload, so here's the link to it: https://drive.google.com/file/d/16dZSFe28WBY1w17XAsEEcX7bEJ7HIF2G/view?usp=sharing

and the update positions file: https://drive.google.com/file/d/1sOQbub7TSXypOoN92ct88wUn3LFNE-VA/view?usp=sharing

[Christopher Chang]

Thanks.  Yes, it turns out this is intended behavior: the --update-map file specifies negative positions for the removed variants.  I'll make sure the .log mentions this in the next PLINK 1.9 build.

[Anna]

Oh! Thank you! I got the position file from somebody else and I didn't even think that there might be negative positions (why?!). Great, that's an easy fix :-D Thanks a lot and yes, if the log could say this is what happened, that would make life easier. :)