Hello,

when running DiscoSNP++ on several datasets where e.g. Reference is C, Dataset 1 is T and Dataset 2 is G at one position, this position is absent from the output files. When running DiscoSNP++ separately on Dataset 1 vs Reference, then on Dataset 2 vs Reference, the polymorphic position is present in both vcf files.

Am I doing something wrong when launching the program or is this case not taken into account?