Viewing RNA-seq data by IGV, I found that position of some indels shifts bases.

Question

[JingxinFu]

Hi, I am trying to view variants, called based on the reference genome, from RNA-seq data by IGV.

For example:

According to the annotation file of variants, the INS should occur at the position where the dash line around. However, the INS indicated from IGV(I) occurs at the position where the red box around.

So, i am confused about the result. Could anyone explain this to me? Thanks!

Answer 1

[Devon Ryan]

Your variant is from a variant caller that's likely making a graph that results in right-aligning matches and therefore places insertions of homopolymer repeats on the left. Your aligner, on the other hand, is placing insertions/deletions of homopolymer repeats on the right. IGV just shows what's in a BAM file, so it's showing what your aligner produced. Of course, the insertion could actually be anywhere between 37008133 and 37008140, it's not possible to tell exactly where the insertion is occurring.