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Funcotator checks the VCF input sequence dictionary to see if it corresponds to the b37 reference so that it can automatically convert b37 variants to hg19.
In the case where a partial b37 sequence dictionary is provided, funcotator should emit a warning message stating that the sequence dictionary could be b37 but because it's incomplete, it cannot do the automatic conversion.
The code that must be changed for this is in FuncotatorEngine::determineReferenceAndDatasourceCompatibility and FuncotatorUtils::isSequenceDictionaryUsingB37Reference.
The text was updated successfully, but these errors were encountered:
Funcotator checks the VCF input sequence dictionary to see if it corresponds to the
b37
reference so that it can automatically convertb37
variants tohg19
.In the case where a partial
b37
sequence dictionary is provided, funcotator should emit a warning message stating that the sequence dictionary could beb37
but because it's incomplete, it cannot do the automatic conversion.The code that must be changed for this is in
FuncotatorEngine::determineReferenceAndDatasourceCompatibility
andFuncotatorUtils::isSequenceDictionaryUsingB37Reference
.The text was updated successfully, but these errors were encountered: