I'm trying to run Variant Effect Predictor (VEP) on TCGA VCF(-like) files that were converted from MAFs. I get the following warnings on insertions: WARNING: Alleles look like an insertion (-/GCAAT) but coordinates are not start = end + 1 (START=56620027, END=56620027) for variant (.) on line 19.
Therefore, the insertions are not present in the output files...
My VCF file looks like the following:
Columns are Chromosome, Start position, ID, Ref. seq, Alt. seq, VAF.
The problem is with the Start position column but I couldn't figure out how to modify it to work. If I'm correct, I should specify the End position as well, but I got no luck in finding the correct format that VEP accepts. Can someone please help me with how to resolve it? Thanks!