Is there any GUI tool which can compare 200 VCFs and show different SNPs between all the samples? Have tried GATK, BCF tools, VarChest, VCFTools, NextGene project comparison, DNAStar, R packages. Is there a better solution available? Thank you.
Using GATK (not a GUI tool) CombineVariants you can read many VCF and combines them into a single VCFs. CombineVariants always produces a union of the input VCFs. Then any part of the Venn of the merged VCFs can be extracted using JEXL expressions on the set attribute using SelectVariants.