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!
why a screenshot when you can just copy+paste the data ?
'-' is not valid: this is not how a indel should be defined in a vcf. https://samtools.github.io/hts-specs/VCFv4.2.pdf
Thanks! I'm pretty new to this website, but it's nice to know that I can paste spreadsheet data!
Yep, my VCF file was not following any possible input format for VEP, that is why it didn't work. Now It works like a charm.
Thanks!