Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Issue about different reference human assemblies #27

Open
anyone1985 opened this issue Jul 25, 2019 · 1 comment
Open

Issue about different reference human assemblies #27

anyone1985 opened this issue Jul 25, 2019 · 1 comment

Comments

@anyone1985
Copy link

Hi,

I'm new for this wonderful tool. When i look up the 00-All.vcf.gz, I think it uses GRCh38.p7 as the reference assembly. While the other databases use Hg19 as the reference. I'd like to know if it is right to use liftover utility to convert genome coordinates from GRCh38 to Hg19.

@Flope
Copy link

Flope commented Sep 10, 2021

I also noticed the inconsistency of the data coordinates in the instructions.
You can get on those DBs the hg19 version of them. For the, dbSNP
wget https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/00-All.vcf.gz --no-passive-ftp

And the ExAC dataset should be this one:
wget https://storage.googleapis.com/gcp-public-data--gnomad/legacy/exac_browser/ExAC.r1.sites.vep.vcf.gz

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants