I have 6 VCF files, where I would like to obtain the SNPs that are common (by position) in all the 6 files. I have tried this command
bcftools isec -p trial2 -n=6 -c all A2_SNP.vcf.gz A_SNP.vcf.gz B_SNP.vcf.gz C_SNP.vcf.gzD_SNP.vcf.gz E_SNP.vcf.gz
But this produces 6 files, and through the README file, I think each of the VCF contains the unique SNPs for each of the 6 files, and I could only get sites.txt file that ocntain the positions that are common. Are there any way to get a VCF file that have the common SNPs ?