Access to public exome files

Question

[storm1907]

Hi,

I am in need to run association tests, such as SKAT, etc, for allelic variant characterization. To do this, I also need to download external control files (exome vcf or txt files) from public databases. I checked UK Biobank and Michigan Genomics Initiative, but it looks that only authorised researchers from UK or USA with special memberships can access to full exome data ( I am not from these countries) NHLBI Exome Sequencing Project (ESP) seems to be appropriate; However, I am curious, if there are more options to get exome recordings without being in partnership with particular database?

Thank you!

[4galaxy77]

1000 genomes and HGDP are bothy publically available.

[storm1907]

Thank you! But these are all genomes; is there a way to convert grch38 genome to exome file type?

[GenoMax]

Since the links are for whole genome sequencing moving this answer to a comment. OP wants exome data.

[4galaxy77]

Fair enough. I've not worked with exome data much - but would it not be trivial to just filter the wgs data for exome regions?

[storm1907]

I am wondering, how to do it Is that possible?

[GenoMax]

It should be possible to access restricted data at NHLBI from countries other then US/UK (barring a few others). It will likely require a eRA commons account and a specific proposal. These would need to be set up at your institutional level (eRA commons) and from a principal investigator (if you are one or otherwise your mentor).

Answer 1

[JC]

if there are more options to get exome recordings without being in partnership with particular database?

human data is restricted because of privacy, so you will not find that anywhere, maybe you can use the exomes in 1000 genomes project.