SarsCov2 annotation database

Question

[ognjen011]

Hello!

When sequencing SarsCov2 viruses we get a number of variants, and it would be interesting to see if these variants are already reported and where, or use it as a filtration criteria. Is there an annotation database, ideally as a vcf like dbsnp, that could annotate resulting mutation VCFs for viral whole genome sequencing?

Thanks!

[GenoMax]

it would be interesting to see if these variants are already reported

They have probably been reported. Question is are they in a place/form that you can query/use. GSAID/NCBI both have thousands of genomes now and since it is only a 29kb genome we should have seen most of changes by now.

Answer 1

[Jean-Karim Heriche]

Look at the COVID19 data portal variants section.

[ognjen011]

Thank you, this is a great suggestion. Still, I can't fine a usable database or VCF file to use wtih an annotator, is there such a thing that you know of? I went further to ensembl, but I don't get around easily there.

Answer 2

[GenoMax]

You could use Ensembl VEP tool with the right data/annotation.

[ognjen011]

Thanks, that is the idea, but I can't find a VCF for that, or do you know how to use a plugin that doesn't require it?

[GenoMax]

If you are not going to have your own VCF to annotate then using a public mutation database like one @Jean-Karim linked would be your best bet.