I am working on multiplex NGS results. I have vcf file which contains a lot of false positive variants. I know they are false positive because they obtain last nucleotide in read (from overlapping reads they are not present). I would like to label those variants. Do you know why I have those variants? I was performing primer trimming by cutadapt.
Those variants only appear in multiplex results. I don't see them in results created by probe (for the same sample).
PS. This could be caused by not performing "marking duplicates", but in multiplex it is impossible to do that.