search

knowledgesystems / signal

Somatic Integration of Germline Alterations in cancer
https://www.signaldb.org/
MIT License
2 stars 5 forks source link

Some new signal mutation is not in initial list of mutations #101

Open leexgh opened 3 years ago

leexgh commented 3 years ago

Some mutations in Chai's new signal files is not in our initial list of signal mutations. For example: the second row in signaldb_variants_by_cancertype_summary_statistics.txt - 9_133710815_133710815_G_T, this variant is currently not in database.

https://www.genomenexus.org/signal/mutation/hgvs/9%3Ag.133710815G%3ET

leexgh commented 3 years ago

From Chai:

And, regarding "9_133710815_133710815_G_T", I am not sure of the source of difference. In any case, these sort of discrepancies should be restricted to VUSs and likely introduced by slight differences in how Preethi (who generated the initial set of variants) and I built the criteria for a VUS/rare-variant. These differences should be very minor and for most part not at all important. However, if these differences are causing issues for you, I can re-generate the earlier set of files we shared with Onur. Let me know.