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.

Sign up for GitHub

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

Jump to bottom

Include GRCh37 allele frequencies from DiscovEHR #315

Closed
katherinesmith opened this issue Feb 7, 2017 · 2 comments
Closed

Include GRCh37 allele frequencies from DiscovEHR #315

katherinesmith opened this issue Feb 7, 2017 · 2 comments
Assignees
@javild
Labels
database enhancement

Comments

@katherinesmith
Copy link

This is an exome sequencing study of 50,726 individuals, including some with diseases. Variants with AF <0.001 are indicated with the INFO tag AF_LT_001 rather than an exact frequency

http://discovehrshare.com/downloads
@javild
Copy link
Member

javild commented Feb 7, 2017 •
edited
Loading

Great, this task requires the following steps:

  • Check biodata is able to parse that frequency format . Biodata is currently not able to parse it. Waiting for Implement parsing of aggregated frequencies as provided by DiscovEHR biodata#144 to resolve
  • Load into OpenCGA installation
  • Export parsed frequencies from OpenCGA installation
  • Annotate CellBase-variation with updated frequencies
  • Replace current CellBase-variation by the new CellBase-variation with updated frequencies

@javild javild self-assigned this Mar 1, 2017
@javild javild mentioned this issue Mar 1, 2017
Open
@javild
Copy link
Member

javild commented Sep 12, 2018

Done.

@javild javild closed this as completed Sep 12, 2018
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@javild javild

Labels
database enhancement
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@katherinesmith @javild