I want to intersect a vcf file with a bed file for which I use the following command:
intersectBed -a vcf -b bedfile > newvcf
The problem here is that the file newvcf is a vcf file without a header so when I want to intersect the two vcfs with this command, I am not able to do that:
vcf-isec -n +2 A.vcf.gz B.vcf.qz | bgzip -c > out.vcf
How I can create the intersect with bed file so I can have a proper vcf file with header as the output?