Evidence information about reported variants

[Sekhar Hari]

Hello there -

Firstly, I will like to congratulate and convey my respect to the people who did this massive work to collect such an important information for further improvement of Medicine.

I just downloaded the VCF file, and glanced through it so far. I have a need to extract some additional (evidence based) information for these variants. Is it possible to enrich this file with the following information for each of the reported variants?

1. Disease name / Trait

2. Pubmed ID where this variant was studied and published (along with a link to the published journal)

3. Mapped gene ID

4. Initial sample size (should include the sample size for both cases and controls)

5. Intergenic (just Yes or No value)

6. Reported risk allele frequency

7. Chromosome region (1q32.1)

8. P-value

9. Odds Ratio or Beta Co-efficient (whichever is applicable)

10. 95 % CI (this is optional though)

Many thanks,

Sekhar H.

[Terry Farrah]

Sekhar,

It is great to hear that you are finding Kaviar useful. Thank you for the list of information you would like to see in our VCF files. We have been discussing how to enrich Kaviar so that users do not need to go to other resources for this sort of thing. It is our desire to enrich the interactive version of Kaviar with at least some of this information (items 1-3, 5); however, due to funding issues, we don't have a timeline for this at the moment.

It is unlikely that we will ever include this information in the VCF because we do not want the file to become too large. However, if there are many requests for an enriched VCF, we may consider it.

I am not sure what you mean by items 4, 6, and 8-10. One of our long-term goals is to develop confidence measures for rare variants. However, I wonder if you are referring to confidence measures for disease associations -- if so, we are unlikely to ever include these in Kaviar. Kaviar's purpose is simply to provide allele frequencies. Other resources are available to describe disease associations.

Thank you again for your communication and we encourage you to write to us with any further questions or suggestions.

Sincerely,

Terry Farrah

Terry Farrah
Bioinformatics Scientist

Institute for Systems Biology
206-732-1348

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