My aim was to get variation information/annotation about some of my genes of interest whose differential expression details I got from their RNAseq data.
Since, my variant calling tool will give information of all non-coding genes and probable unknown genes as well, I decided to annotate the variants (which were called using RNAseq reads) using SnpEff with -onlyprotein option (meaning-Only use protein coding transcripts). The reason was that, it will only annotate the variants that arose from transcripts from protein coding genes and not from anywhere else. But, I got variants annotated that were in downstream gene variant/intergenic that is not possible.
I have already asked about 'downstream gene variant/intergenic' issue in another post (https://www.biostars.org/p/239773/#239965), the reason about this post is if I have understood '-onlyprotein ' option wrong and if its ok to get the results I am getting.