I am working on produced VCF files from whole exome sequencing prostate cancer patients using MuTect2. I have compared normal/tumor matched samples and found mutations. During library preparation, we used a kit for exome capture (SureSelect Human All Exon V6). Next, I wanted to perform a functional prediction of these variants using SnpEff tool (http://snpeff.sourceforge.net/index.html). The reference genome is hg19 which I used to annotate my samples. Below, I am posting a screenshot of IGV as example showing the different builds for one random reported variant.
Now that being said, what I expect when I get a report of SnpEff is that CDK11B should have a functional impact on the exon if it was annotated with GRCh37.75 because the variant comes within the exon. And this is the case of many variants. However, below I am showing you a screenshot when I annotated the sample with the two builds:
Inspecting in details this particular variant, I found:
So why is SnpEff reporting variants that comes into exons as intron variants ?
Thank you in advance.