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InPreD / PRONTO

rePort geneRator fOr iNpred Tumor bOards
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Tumor content number provided multiple times for one sample set #37

Open tinavisnovska opened 4 months ago

tinavisnovska commented 4 months ago

Hi! There are two different ways in which tumor content is provided to PRONTO: 1) via TSOPPI results and 2) via PRONTO metadata file. When the two numbers do not agree, PRONTO takes the number from the 1) option and fills that one into the report. I do not see any trace of PRONTO rising this as an issue (no warning, no error in any of the logs).

It would be good either to eliminate the redundancy in how many times the tumor content is provided to pronto or add a check and inform the user that there is such an inconsistency. It would also be useful to document all the inputs that PRONTO uses and how they are used.

tinavisnovska commented 4 months ago

The number in option 1) is taken from the small variant table,...

xiaoliz0 commented 3 months ago

Sorry for the late replying. Emm, this was discussed before I think. PRONTO works based on the TSOPPI results, and the tumor content is taken from the TSOPPI results since it is the "real" number in analysis. The meta file is used to give the clinical data which TSOPPPI could not provide. The tumor content column in meta file is used to record the number from lab. So you could check and see the difference if you want.

tinavisnovska commented 3 months ago

Hello again ;), chances are that this was discussed before, but as long as description of the behavior is not documented anywhere findable in the repository or related documentation, or incorporated in the code itself one can expect that the issue will be raised again and again as the behavior is not very intuitive.

Even though TSOPPI reports tumor content in the output files, it also (similarly to PRONTO) gets the tumor content value as an input provided by a person running the analysis - TSOPPI is not doing any calculations or estimates of that value - it gets the value as an input and prints it to the output without any change - so it is (at least in our case) the same number recorded in the lab. I remember now that you sometime adjust the tumor content according to copy number plots and rerun TSOPPI - so I take it that from that perspective it does not make sense to call it an error if the two tumor content values are not the same. However, it might be rather useful to rise a warning there saying that the two values differ, one of them is provided via the metadata file is X and the other one written in the TSOPPI output file A is Y. Otherwise it takes ages to figure out what is going on...