Does someone know how to disable intragenic flag in snpeff annotation like for upstream downstream splice exon etc? I know that there is a description about intragenic variant in snpeff website. However, I noticed that these variants are falling in intergenic, intronic or utr regions of non coding genes and I would like to set priority on these annotations over the intragenic.
Any suggestion is appreciated.
No need to suggest me other annotation tools, as I am aware of them. I just need a potential solution to my specific question.