I have the following files:

1. A.vcf which contains one sample s1
2. B.vcf which contains one sample s1
3. region.bed

I'd like to merge A.vcf and B.vcf for sites in region.bed, and use A.vcf for sites present in both files. Here is my command but it does not work as I expected:

bcftools isec A.vcf.gz B.vcf.gz -R region.bed -n+1 -o tmp.vcf.gz -O z -c all -w1

Could anyone help?

Thanks a lot!