I am trying to merge two GWAS data sets in Plink. Apparently there are multiple variant ids that share the same position but have different alleles. The merge command then errors out. I wish it would cycle through the remaining file and generate a whole list of these so that I could exclude them all at once. Does anyone know how to code this?
C:\Python27\Scripts>plink --bfile AABC_Ziv_Shanghai2 --bmerge CIDR_chr1_cleaned --make-bed --out CIDR_chr1_AABC_Ziv_shanghai --merge-equal-pos
PLINK v1.90b3.27 64-bit (13 Dec 2015) https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to CIDR_chr1_AABC_Ziv_shanghai.log.
Options in effect:
7944 MB RAM detected; reserving 3972 MB for main workspace.
6320 people loaded from AABC_Ziv_Shanghai2.fam.
4001 people to be merged from CIDR_chr1_cleaned.fam.
Of these, 4001 are new, while 0 are present in the base dataset.
1449016 markers loaded from AABC_Ziv_Shanghai2.bim.
176885 markers to be merged from CIDR_chr1_cleaned.bim.
Of these, 143496 are new, while 33389 are present in the base dataset.
Warning: Variants 'rs3094315' and '1:752566' have the same position.
Warning: Variants 'rs4040617' and 'kgp5225889' have the same position.
Warning: Variants 'rs28609852' and 'kgp3324955' have the same position.
Error: --merge-equal-pos failure. Variants 'rs17026104' and 'kgp4275897' have
the same position, but do not share the same alleles.