I'm trying to merge 2 whole-genome vcf files with different individuals with
The program generates seems to merge both files but, surprisingly, it puts a
./. in all the SNPs of the second file (as if they hadn't been genotyped, but they have!)
I've also tried to merge both files using
bcftools merge but my command returns the following:
The REF prefixes differ: GC vs C (2,1)
Failed to merge alleles at chrM:16375063 in myfile.vcf.gz
I've read in this post that I can silence this error by using
bcftools +fixrefplugin, but I don't actually understand what it does, as it asks you to give a reference data file to obtain missing data from there.
If anyone could help with any of both options, I'd be really grateful! Thank you very much in advanced!