Corrections made by batch name checker not indicated
Created by: mutalyzerbot
Original ticket: https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/162 Original date: 2014/02/07 Original reporter: martijn
It is not directly clear from the result file when the batch name checker has made any corrections to the input.
For example, NM_000088.3:c.3802_3805delGACT
will be corrected to NM_000088.3(COL1A1_v001):c.3803_3806del
with a warning
Sequence "GACT" at position 3928_3931 was given, however, the HGVS notation prescribes that on the forward strand it should be "ACTG" at position 3929_3932
which is shown in the interactive website interface, but not in the batch name checker result file.
The origin of this discrepancy it that many warning messages can be issued by the name checker which need not all be informative to the batch name checker user (e.g., when the concern the reference sequence or even unrelated transcripts therein). Therefore we decided some time back to decrease the amount of messages shown in the batch result file. Obviously, this has unintended effects.
I see several ways to improve (not all mutually exclusive):
- Add some explanation to the batch interface ('warnings are not shown' or similar).
- Include all warnings and errors.
- Add a new boolean column to the result file stating whether the input variant has been corrected or remained unchanged. This not as straightforward as comparing two columns (input/output), since the output can contain several descriptions and we don't know which one should correspond to the input.