Closed snehaleela closed 11 months ago
whaleyr
commented
1 year ago Can you supply an example VCF file that demonstrates the problem?
Please make sure this is not an actual sample file with any personally identifiable information and truncated to as small of a dataset as possible.
snehaleela
commented
1 year ago Hi we have used the VCF's provided in Pharmcat github page only : For VKORC1 - -1639A-1639A.vcf - rs9923231 reference(C)/rs9923231 reference(C) -1639G-1639A.vcf - rs9923231 reference(C)/rs9923231 reference(T) - Correct -1639G-1639G.vcf - rs9923231 reference(C)/rs9923231 reference(C)
whaleyr
commented
1 year ago I'm still having a hard time understanding.
The files you're pointing out are resource files used for running a unit test in the codebase.
In those unit tests you can see the expectedMatches List contains what we expect each file to report. All those unit tests pass in the current version of PharmCAT. Those diplotype strings are what we expect the calls to be.
rs9923231 reference(C)/rs9923231 reference(T) is not correct because reference(T) doesn't make sense. T is the variant allele at this position so it would be labeled as variant, not reference. The correct call is rs9923231 reference (C)/rs9923231 variant (T).
Backing up a bit, can you describe what you're trying to do at a higher level? Are you trying to run existing unit tests in PharmCAT for yourself? Are you taking out those unit test resource files and trying to use them in a different context? Knowing what you're trying to do may help us give you better feedback.
markwoon
commented
11 months ago Closing issue due to insufficient information.
@snehaleela We need more information in order to help you. Feel free to re-open this issue if you can provide the details Ryan is asking for above.
Do you want to request a feature or report a bug? Bug
What is the current behavior?
UGT1A1 - Genotype output - 1/1 - For newer version of pharmcat - 2.6.0 VKORC1 - Genotype output - rs9923231 reference(C)/rs9923231 reference(C) - For newer version of pharmcat - 2.6.0
UGT1A1 - Genotype output - 80+28/80+28 - For older version of pharmcat - 2.1.2 VKORC1 - Genotype output - rs9923231 reference(C)/rs9923231 reference(T) - For newer version of pharmcat - 2.6.0
UGT1A1 - Genotype output - 80+28/80+28 VKORC1 - Genotype output - rs9923231 reference(C)/rs9923231 reference(T)
What is the motivation / use case for changing the behavior?
Please tell us about your environment:
Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, e.g. stackoverflow, gitter, etc.)