Plink merge errors.

Question

[Dinmukhamed]

Hello!

Right now I am having trouble with merging multiple bed, bim, fam files.

Here is my code:

$ ./plink.exe --bfile 1data --merge-list merge.txt --dog --make-bed --out merged
Options in effect:
  --bfile 1data
  --dog
  --make-bed
  --merge-list merge.txt
  --out merged
16221 MB RAM detected; reserving 8110 MB for main workspace.
Warning: Multiple positions seen for variant ...
Warning: Multiple chromosomes seen for variant ...
218647 more multiple-position warnings: see log file.
Error: 18464 variants with 3+ alleles present.
If you believe this is due to strand inconsistency, try --flip with
  merged-merge.missnp.

Then I tried from https://www.cog-genomics.org/plink/1.9/data#merge3:~:text=plink%20%2D%2Dbfile%20source2,out%20source2_corrected

Next I tried --flip and I lost some data. What I should do? Do I need to use this code lines

plink --bfile source2 --flip merged.missnp --make-bed --out source2_trial
plink --bfile source1 --bmerge source2_trial --make-bed --out merged_trial
plink --bfile source2_trial --flip merged_trial.missnp --make-bed --out source2_corrected

Thanks!

Answer 1

[Dinmukhamed]

I found answer Accounting for problem SNPS when merging multiple plink files.