Run a duplicate variant through the pipeline, once with the correct genename and once with an outdated one, for instance
KMT2D and MLL2.
Example variant: 12:49440141-49440141 G>C on KMT2D (previously MLL2)
Expected:
Variant is reported as duplicate and written to the errorfile
Observed:
Duplicate variant determination is done before gene translation, so the file gets correctly translated and therefore is reported twice in the output file.
Run a duplicate variant through the pipeline, once with the correct genename and once with an outdated one, for instance KMT2D and MLL2.
Example variant: 12:49440141-49440141 G>C on KMT2D (previously MLL2)
Expected: Variant is reported as duplicate and written to the errorfile
Observed: Duplicate variant determination is done before gene translation, so the file gets correctly translated and therefore is reported twice in the output file.