Cyriac Kandoth

https://linkedin.com/in/ckandoth [email protected]

Penn Medicine Perth, WA, Australia I'm an engineer that studies the pathogenesis of genetic diseases like cancer, in search of druggable targets, early diagnosis, and prevention.

Results 16 issues of


                                            Cyriac Kandoth

Add more sample-level information for display in cBioPortal

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Add more columns to data_clinical.txt, using http://oncotree.mskcc.org/cdd/api/ to standardize column names if possible. - [ ] `MOUSE_CONTAMINATION` - For batches with at least 1 PDX sample, report fraction of sequenced...

Calculate and add TMB into data_clinical file

Do TMB calculation like DMP does (number of non-silent somatic events in analysis MAF ÷ number of bps in canonical exons covered by assay), and append to data_clinical using nomenclature...

Retroactively fix clinical data columns for cBioPortal

- [x] Use http://oncotree.mskcc.org/cdd/api/ to update column header descriptions and metadata. - [x] Swap `SAMPLE_TYPE` and `SAMPLE_CLASS` if appropriate. Refer to https://github.com/mskcc/roslin-internal-services/issues/6 for description of the problem. - [ ]...

Run MSIsensor and add result into data_clinical

Run "msisensor msi" with 35M sites using both v0.2 and v0.6, and append results into data_clinical using nomenclature recommended in http://oncotree.mskcc.org/cdd/api/

Optimize Abra parameters for somatic calling

Per author suggestions at - https://github.com/mozack/abra2/issues/21#issuecomment-409657543 - of relevance: We have not done thorough testing with anything beyond trios to date. Also, the local assembly graph is not allowed to...

Quantify drawbacks of limiting Abra to coding regions

As of Roslin 2.4.2, we run Abra per pair, but we used to run it per group. On a project where Abra operated on 5 BAMs at a time from...

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