Is your feature request related to a problem? Please describe.
Stranger sets str_status based on the count of pathogenic motifs in a repeat, but does not write the actual count in the output VCF. This makes it hard to see what number str_status is based upon. In the current implementation at clinical genomic, Scout has it's own counting function, the issues with this are described here: Clinical-Genomics/scout#5528
Describe the solution you'd like
I would like Stranger to output the pathogenic count in the output VCF, so that the counting function in Scout can be removed. Reducing complexity, the chance for mistakes and code duplication in the current Stranger-Scout implementation.
Describe alternatives you've considered
Keep it as it is.
Additional context
Should investigate how this works with TRGT v3.
Is your feature request related to a problem? Please describe.
Stranger sets
str_statusbased on the count of pathogenic motifs in a repeat, but does not write the actual count in the output VCF. This makes it hard to see what numberstr_statusis based upon. In the current implementation at clinical genomic, Scout has it's own counting function, the issues with this are described here: Clinical-Genomics/scout#5528Describe the solution you'd like
I would like Stranger to output the pathogenic count in the output VCF, so that the counting function in Scout can be removed. Reducing complexity, the chance for mistakes and code duplication in the current Stranger-Scout implementation.
Describe alternatives you've considered
Keep it as it is.
Additional context
Should investigate how this works with TRGT v3.