Sources Of Publicly Available Human Whole Genome Sequence Data

Question

[Alex Paciorkowski]

We're looking for publicly available human whole genome sequence data for the purposes of filtering variants out of our local data. We're primarily analyzing the exome from WGS data, but are also developing a non-coding analysis pipeline.

I am aware of the data offered by Complete Genomics here, and of course, 1000 Genomes.

Is anyone aware of other similar public sources of data? Thanks.

Answer 1

[Prateek]

TCGA hosts canacer sequencing data: https://tcga-data.nci.nih.gov/tcga/

COSMIC again is a database of cancer mutations but also includes those identified as germline mutations: http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/

[Alex Paciorkowski]

Thanks, Prateek. I'll check these out. Not being a cancer geneticist, I'm not aware of all the resources on that side of the street, but in general it appears cancer researchers have larger repositories of WGS data at this point.

Answer 2

[JC]

if you just want a compilation of several sources you can try: http://db.systemsbiology.net/kaviar/

[Alex Paciorkowski]

Thanks, Juan. We've used Kaviar for selected batches of variants, but it looks like the entire dataset can be downloaded locally. Do you know how much overlap there is with NHLBI's exome variant server?

[JC]

Alex, yes you can install and run locally Kaviar, we used the Perl Module in our analysis scripts. The lastest version of Kaviar has all the NHLBI's variants.