Is there a way to compare more than two vcf files (around 50) with vcftools with the command below?
vcftools 1.vcf --diff 2.vcf
The reason that I am using this --diff option is because I am interested to get the matrix/table that shows the difference of the genotype output from my vcf files (just like the output of out.diff.sitesinfiles) So far, I am only able to compare two files.
Ideally, I would like to get a matrix that would look like this
Chr Pos Ref ALT1 ALT2 ALT3 ........ALTn
Appreciate your inputs
Thanks in advance.