I am looking for a tool that collects common variants from multiple VCF files (more than 30 files) the only tool I could find so far is findcommonvariants from Rsubread package, but it has two problems:
- it completely ignores the last input, ex. if I put (A.vcf, B.vcf , C.vcf) it compares only between A and B
ABC = findCommonVariants(c(A,B,C)) >> MA01vs03 = findCommonVariants(c(A,B,C)) Process file A There are 106 variants found in this file. Process file B There are 91 variants found in this file. Finished! There are 5 common variants from the 2 input files.
- even when it says 5 common variants, it only shows 3 variant (-2 of the actual written number)
Anybody knows how to fix that, or if there is a better tool to do this comparison?