Hi,
I'm annotating my VCF using VEP. By default, VEP generates an output with variants only. So positions with no variation are not reported. I can add non-variant positions by adding --allow_non_variant tag but I cannot get INFO section for these positions. I want to have at least the gene HGNC name/symbol for those positions. Is it possible?
Thank you for your answers!
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magnolia •
Thank you for the explanation. I know that the whole point of CSQ section is consequences of the variant. I just need to add information to non-variant positions as well. So I'm guessing it's impossible with VEP?
Because I also want to see what positions are covered in the VCF and which genes are in those positions.
For example, let's say I have a VCF file that contains 10 positions for BRCA1 but only one of them is a variant. Since I cannot keep every single gene's location in the genome in my mind, when I filter for BRCA1, I will get that 1 variant but I also want to see which other positions are covered for BRCA1 in the VCF.
I can just generate synthetic data in, lets say, tsv/txt and then convert it to VCF and then load into VEP. This part, in my opinion, doesn't matter. As VEP being variant effect predictor, I guess there is no flexibility for that. I cannot get any information for a position that is not a variant.
But since you mentioned, gVCF, what if I'm using that then? Is there a workaround?
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Do you mean you already have HGNC IDs in the INFO field that are being omitted by VEP or that you'd like VEP to add HGNC symbols to all positions including non-variant positions?
I would like to add HGNC symbols to all positions including non-variant positions. This is the most crucial one but if possible, whatever custom database I give to VEP, I want to see the matched INFO in every position.