I have thousands of vcf which I want to merge into just one vcf. For that purpose, I am using vcftools.
bcftools merge --force -l list_files_to_merge -Oz -o ./Merged.vcf.gz
--force is used because in some vcf files some samples may be repeated. I do not care about that.
The command works but it stops when one reference does not match the reference with other samples. That will probably mean that this vcf used another reference genome that is ok.
The REF prefixes differ: T vs A (1,1) Failed to merge alleles at X:15517198 in file_5000.vcf.gz
I would like to have the possibility of omitting this vcf (file_5000.vcf.gz in the example) and continue with the merge command. Maybe in the log file it may be written which samples were omitted due to this error.
Is there a way for doing this?