Frequently asked questions regarding PCGR usage and functionality:
1. I do not see any data related to allelic depth/support in my report. I thought that PCGR can grab this information automatically from my VCF?
Answer: VCF variant genotype data (i.e. AD/DP) is something that
you as a user need to specify explicitly when running PCGR. In our
experience, there is currently no uniform way that variant callers
format these types of data (allelic fraction/depth, tumor/normal) in the
VCF, and this makes it very challenging for PCGR to automatically grab
this information from any VCF. Please take a careful look at the example
VCF files (examples folder) that comes with PCGR for how
PCGR expects this information to be formatted, and make sure your VCF is
formatted accordingly. There is also an in-depth explanation on the
matter described
here
2. Is it possible to utilize PCGR for analysis of multiple samples?
Answer: As the name of the tool implies, PCGR was developed for the detailed analysis of individual tumor samples. However, if you take advantage of the different outputs from PCGR, it can also be utilized for analysis of multiple samples. First, make sure your input files are organized per sample (i.e. one VCF file per sample, one CNA file per sample), so that they can be fed directly to PCGR. Now, once all samples have been processed with PCGR, note that all the tab-separated output files (i.e. annotated SNVs, gene copy numbers) contain the sample identifier, which enable them to be aggregated and suitable for a downstream multi-sample analysis. Also note the multi-sheet Excel workbook, which contains numerous outputs from PCGR, and can be processed to aggregate findings across samples.
3. I do not see the expected transcript-specific consequence for a particular variant. In what way is the primary variant consequence established?
Answer: PCGR relies upon VEP for consequence prioritization, in which a specific transcript-specific consequence is chosen as the primary variant consequence. In the PCGR configuration file, you may customise how this is chosen by changing the order of criteria applied when choosing a primary consequence block - parameter vep_pick_order
4. Is it possible to use RefSeq as the underlying gene transcript model in PCGR?
Answer: PCGR uses GENCODE as the primary gene transcript model, but we provide cross-references to corresponding RefSeq transcripts when this is available.
5. I have a VCF with structural variants detected in my tumor sample, can PCGR process those as well?
Answer: This is currently not supported as input for PCGR, but is something we want to incorporate in the future.
6. Is it possible to see all the invididual cancer subtypes that belong to each of the 30 different tumor sites?
Answer: Yes, see an overview of phenotypes associated with primary tumor sites. See also the related GitHub repository phenOncoX
7. Are there any plans to incorporate genomic biomarker evidence from OncoKB in PCGR?
Answer: No. PCGR relies upon publicly available, open-source resources, and further that the PCGR reference bundle can be distributed freely to the user community. It is our understanding that OncoKB’s terms of use do not fit well with this strategy.
8. I have RNA fusion data that I want to analyse and include in the report. Is this possible with PCGR?
Answer: This is currently not supported as input for PCGR, but is something we are actively working on. The focus will be on whether detected RNA fusion events are previously known (i.e. seen in other tumor samples, e.g. from the Mitelman database), and whether some of them are presently in use as biomarkers for diagnosis or treatment.
9. Is it possible for the users to update the data bundle to get the most recent versions of all underlying data sources?
Answer: As of now, the data bundle is updated only with each release of PCGR. The data harmonization pipeline of knowledge databases in PCGR contain numerous and complex procedures, with several cleaning, quality control, and re-formatting steps, and is semi-automated in its present form. The version of all databases and key software elements are outlined in each PCGR report.