vafcorrect will miss the reads where read has only soft-clipped bases within the 'region' considered for overlapping read retrieval. Possible fix is to extend 'region' boundaries: https://github.com/cancerit/vafCorrect/blob/22b2b332d6421e40e96870ea732781aa54314237/perl/lib/Sanger/CGP/Vaf/Process/Variant.pm#L572