I am comparing five vcf files each with multiple samples using
bcftools isec -p dir -n=5 a.vcf.gz b.vcf.gz c.vcf.gz d.vcf.gz e.vcf.gz
It results in these files:
0000.vcf 0001.vcf 0002.vcf 0003.vcf 0004.vcf README.txt sites.txt
However, the output does not show intersection sites among all five vcf files. I am not sure if something is wrong in the command line. I will appreciate any suggestions. Thank you.