I have the following files:
A.vcfwhich contains one sample s1
B.vcfwhich contains one sample s1
I'd like to merge
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!