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BaderLab / GenomeClinic-PGX

Web application for clinical pharmacogenomic interpretation
GNU Lesser General Public License v3.0
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Variant Issues #105

Closed patmagee closed 9 years ago

patmagee commented 9 years ago

Extra Variant Annotation

At the moment, we are essentially throwing out any non annovar annotation, this can have the side effect of losing a lot of information. Should this data be kept? Processing and storing versions of the build.

We are at a transition phase. People are starting to use GRC38/hg38 over GRC37/hg19. How will we address this? the pgx system will have to be adapted in order to reflect the changes in the build versions and position of the reference genomes. Should we support multiple reference builds and have the user indicate which build to use? we cannot reliably assume reference build information will be included within the vcf format so there is no way for us to determine really if it is a specific build version.

patmagee commented 9 years ago

There has been several issues with uploading vcf files and viewing the pgx data. Some of the alleses will appear missing when they should not be. This could potentially be a result of modifications mad to the allele, or addtitionally it could be a problem with the vcf file itself

patmagee commented 9 years ago

Issue has been moved to #137