Question: Sources Of Publicly Available Human Whole Genome Sequence Data
3
gravatar for Alex Paciorkowski
6.8 years ago by
Rochester, NY USA
Alex Paciorkowski3.3k wrote:

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.

data next-gen • 6.7k views
ADD COMMENTlink modified 14 months ago by Biostar ♦♦ 20 • written 6.8 years ago by Alex Paciorkowski3.3k
2
gravatar for JC
6.8 years ago by
JC7.4k
Mexico
JC7.4k wrote:

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

ADD COMMENTlink written 6.8 years ago by JC7.4k

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?

ADD REPLYlink written 6.8 years ago by Alex Paciorkowski3.3k

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.

ADD REPLYlink written 6.8 years ago by JC7.4k
1
gravatar for Prateek
6.8 years ago by
Prateek1000
Boston, MA
Prateek1000 wrote:

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/

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Prateek1000

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.

ADD REPLYlink written 6.8 years ago by Alex Paciorkowski3.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1297 users visited in the last hour