I used SNPeff to annotate horse SNPs and Indels and found a strange phenomena in the html output.
The number of variants (before filter) is larger than the number of lines (which I understand as being the number of SNPs or indels). That is, the number of variants that get analyzed by SNPeff is larger than the number of variants that are actually in the vcf file itself. I don't know where does SNPeff come up with the extra set of variants. I tried to understand this issue by myself but couldn't really wrap my head around it. I would have given an example HTML here but I couldn't see an option to upload one. I would really appreciate any thoughts or ideas as to why this is the case ?.