Variation Annotation Integrator dbSNP IDS

[Grewal, Marcus]

Hello,

I have recently used the VAI tool to produce a list of known SNPs from a VCF file I uploaded. I was very pleased by how quick and easy the tools was. However, it only gave me the data for SNPs on the X and Y chromosomes.

Is there any way to get the data from all the chromosomes? I know the VCF file I uploaded spanned the whole genome. There is probably a simple field I overlooked​. 

Any help would be greatly appreciated,

-Marcus

[Christopher Lee]

Hi Marcus,

Thank you for your question about annotating snps for the entire
genome instead of just chrX and chrY. There is a "region to annotate"
dropdown that you can change to "genome" to annotate the entire
genome. You may also want to check that the "maximum number of
variants to be processed: " field is able to account for all of the
variants in your VCF.

Please let us know if this solves your problem.

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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