Is your feature request related to a problem? Please describe.
Generally it is a Good Idea that the STR caller identifies the number of reference copies detected given a reference genome, locus catalog and caller version. But we could certainly have a fallback when these are missing, e.g. TRGT
PacificBiosciences/trgt#71.
Describe the solution you'd like
Parse a default REF entry from locus catalogs and use it for output iff there is no INFO.REF field set for the variant.
Describe alternatives you've considered
Stranger could in principle calculate this from the reference region and allele structure definition given, but for more complex cases would need a reference genome sequence, and this baseline guesstimate could deviate from the implementation in the caller.
Is your feature request related to a problem? Please describe.
Generally it is a Good Idea that the STR caller identifies the number of reference copies detected given a reference genome, locus catalog and caller version. But we could certainly have a fallback when these are missing, e.g. TRGT
PacificBiosciences/trgt#71.
Describe the solution you'd like
Parse a default
REFentry from locus catalogs and use it for output iff there is noINFO.REFfield set for the variant.Describe alternatives you've considered
Stranger could in principle calculate this from the reference region and allele structure definition given, but for more complex cases would need a reference genome sequence, and this baseline guesstimate could deviate from the implementation in the caller.