Merging plink files

[George Wanjala]

Dear Chris

I am trying to merge 2 files, ovine geno files, one was genotyped based on reference genome Oar v3.1 (Source.1 file)  while the second one (source.2 file) was genotyped based on Oar v1. Each file has a genotyping rate of > 98%, however, when I merge them,  despite some few warnings of variants in multiple positions, the files successfully merge, but with a genotyping rate of less than 50%. When i Do QC --mind 0.1 and --geno 0.1, all  individuals source 2 file are excluded. All my files are in binary format bed, bim and fam.

What could be the reason for and remedy this?

One type of output is here

PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to XXXX.log.

Warning: Variants 's64199.1' and 's64199' have the same position.
Warning: Variants 'OAR19_64675012.1' and 'OAR19_64675012' have the same
position.
Warning: Variants 'OAR19_64715327.1' and 'OAR19_64715327' have the same
position.
47429 more same-position warnings: see log file.
Performing single-pass merge (75 sheep, 100903 variants).
Merged fileset written to _Merged-merge.bed +
Merged-merge.bim + Merged-merge.fam .
100903 variants loaded from .bim file.
75 sheep (0 males, 0 females, 75 ambiguous) loaded from .fam.
Ambiguous sex IDs written to Merged.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 75 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.491164.
100903 variants and 75 sheep pass filters and QC.
Note: No phenotypes present.
--make-bed to Merged.bed + Merged.bim +
Merged.fam ... done.

 

Please advise.

Regrads

[Christopher Chang]

https://groups.google.com/g/plink2-users/c/mor0GJwmRzc/m/VkFZbw3hCgAJ