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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
74 stars 18 forks source link

Silently missing values when using integer format in rank model and encountering a float value #128

Open Jakob37 opened 5 months ago

Jakob37 commented 5 months ago

We had an issue where some GATK only structural variants did not obtain a rank score.

Looking closer, we found that we had mistakenly specified "integer" as format on GATKs quality GQC field and specified integer ranges.

Some of the GATK GQC values were actually floats. These silently got no rank scores.

It would be useful to get complaints from Genmod when encountering values of formats outside those written in the rank model.

I wanted to share the info as it might save someone else some headache.

henrikstranneheim commented 5 months ago

Thanks for the feedback. Our main developer is currently on parental leave until the fall. So this'll probably be on hold until then. We are also focusing our efforts creating a new app which will replace genmod and use more sophisticated prioritization models.

Jakob37 commented 5 months ago

Thanks for the feedback. Our main developer is currently on parental leave until the fall. So this'll probably be on hold until then. We are also focusing our efforts creating a new app which will replace genmod and use more sophisticated prioritization models.

I see, thanks for the information!