Open rjsicko opened 7 years ago
Thanks for the comments. We will implement this change.
On Thu, May 4, 2017 at 1:10 PM, rjsicko notifications@github.com wrote:
Hi, thanks for the great program! It would be great if the database_names for annovar were read from the config.ini file instead of hard-coded into Intervar.py. This would allow use of the updated databases avsnp147, dbnsfp33a, clinvar_20170130 and incorporation of gnomad_exome, mcap, revel.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/15, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuGbde9V-svfj2Za60wBhjJfKdwPmks5r2gaLgaJpZM4NQ9hU .
Has this been implemented yet? I may be wrong but It still appears that databases are hard coded into Intervar.py.
The user directly change the database name will bring some problem.
I don’t suggest the user direct change the dataset name to update.
Because some intervar pre-built database is more sensitive to some databases, such as clinvar.
What I mean is: the version of intervar prebuilt dataset should come with the same version of outside dataset.
Thanks! Hopefully there will be an updated version at some point that allows other databases to be used.
The user directly change the database name will bring some problem. I don’t suggest the user direct change the dataset name to update. Because some intervar pre-built database is more sensitive to some databases, such as clinvar. What I mean is: the version of intervar prebuilt dataset should come with the same version of outside dataset.
Is dbnsfp33a sensitive to change, ANNOVAR has released the 35a version, which I notice two have 4 more extra columns (not documented on their website tho)? Thanks
Hi, thanks for the great program! It would be great if the database_names for annovar were read from the config.ini file instead of hard-coded into Intervar.py. This would allow use of the updated databases avsnp147, dbnsfp33a, clinvar_20170130 and incorporation of gnomad_exome, mcap, revel.