I have two VCF and I want to find common rsids in those two files. For this purpose I have used grep command by taking list of rsids from one file and running it on other file, but it gave me some extra rsids as well which were not present in the list. I have also used bcftools isec command but it did not give me anything in intersected file. I have also used vcf-isec but it is giving me error of mixed vcf formats. I have checked my files, one file is in v4.1 and other is in v4.2.
Please tell me what should I do to find common rsids in both files?