Human genome variant databases

Question

[johnathan]

We are running a project on data from 1000 genomes and encountered a phenomenon that we'd like to check that it's not an artifact of 1000 genomes. Are there any human variant databases besides 1000 genomes? Edited: I'm looking for a data set of subjects and their variants like the vcf file supplied by 1000 genomes.

[WouterDeCoster]

You are rather vague about what you are searching for, maybe ExAC? http://exac.broadinstitute.org/ It never hurts to share more information with us, it can only improve the accuracy of our answer(s)

[Pierre Lindenbaum]

the 1000 genomes vcf files ?

[johnathan]

Precisely like the VCF file provided by 1000 genomes.

Answer 1

[lakhujanivijay]

You can look at the following databases:

1. DGV Database of Genomic Variants: http://dgv.tcag.ca/dgv/app/home

2. DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) :https://decipher.sanger.ac.uk/about#overview

3. DGVa Database of Genomic Variants (archive): http://www.ebi.ac.uk/dgva

Answer 2

[Giovanni M Dall'Olio]

Have a look at the EBI's Variation Archive (EVA): http://www.ebi.ac.uk/eva/?Study%20Browser&browserType=sgv

Some datasets you may use: - Genomics of the Netherlands - HipSci?

If you give us more information on the type of artifacts you have found, we can help you better.

Note that the EVA version of 1000G is curated, so you may want to check if your artifacts is also present in their data.

[johnathan]

We don't know but the data is behaving in a peculiar way and we'd like to see if this behavior repeats itself in other data sets as well. I'm looking for a data set that provides a list of subjects, a list of genomic locations, the ref seq and the seq the subject actually has. Similar to the data in the VCF file provided by the 1000 genomes project.

[Giovanni M Dall'Olio]

In this case you may be able to find a dataset in EVA.