Entering edit mode
6.3 years ago
bioguy24
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230
I am looking for a tool or script to perform variant prioritization on annotated data from annovar. Currently, I have a script that will classify based on information in the annotation but would like to add a priority score or call to the data as well. I know that is much detail but I guess I am looking for a place to start as I have not found anything. Thank you :).
Priority score or call based on what criteria?
Using the data within the annovar annotation, for example population frequency and clinvar are used in the classifier but maybe I need to expand on that and use inheritance or phenotype? Maybe another column with the score. Just an idea not even sure if I am on the right track though. I wrote an awk script (probably with errors and will post in a few as an example. Thank you :).
The below awk is an example of what I was thinking but not really sure. Thank you :).
Since you are designing this score go for it if it suits your requirements.
Are there additional tools/resources that you recommend? Thank you :).
As above, if this works, then use it - no need to share here (?).
Also, do not try to re-invent the wheel when many of the major players in the clinical genetics scene (biased toward USA) have already voiced their opinions on how to prioritize variants: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology