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Variant Effect Predictor (VEP) warning on insertions: coordinates are not (start = end + 1)

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:

VCF-like file

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!

vcf vep
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written by beketamas • beketamas

why a screenshot when you can just copy+paste the data ?

My VCF file looks like the following

'-' is not valid: this is not how a indel should be defined in a vcf. https://samtools.github.io/hts-specs/VCFv4.2.pdf

For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field)

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written by Pierre Lindenbaum Pierre Lindenbaum

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!

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written by beketamas • beketamas

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