Pathogenic variants don't have statistics summary data

knowledgesystems / signal

Somatic Integration of Germline Alterations in cancer

https://www.signaldb.org/

MIT License

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Pathogenic variants don't have statistics summary data #105

Closed leexgh closed 3 years ago

leexgh commented 3 years ago

Tthere are 1919 pathogenic variants (from biallelic_by_tumortype_merge.txt and mutations_cnv_by_tumortype_merge.txt). None of them are insignaldb_variants_by_cancertype_summary_statistics.txt contains statistics summary data.

It's a data issue, will wait for Chai's response.

TODO:

[x] Update genome nexus importer
[x] Update database
[x] Enable additional columns back

leexgh commented 3 years ago

From Chai:

And, Sorry for the delay on this. I just got around to looking into this and fixing it. Can you pull the updated input files from /juno/work/ccs/bandlamc/shared/signaldb . (Turns out I was excluding the pathogenic variants; that is why these were missing).

leexgh commented 3 years ago

We need to update the data and enable these columns back