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WGLab / InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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FR - Read annovar database names from config.ini #15

Open rjsicko opened 7 years ago

rjsicko commented 7 years ago

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.

kaichop commented 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.

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drmurdock commented 6 years ago

Has this been implemented yet? I may be wrong but It still appears that databases are hard coded into Intervar.py.

quanliustc commented 6 years ago

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.

drmurdock commented 6 years ago

Thanks! Hopefully there will be an updated version at some point that allows other databases to be used.

vnttung commented 5 years ago

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