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HGVS variant nomenclature checker
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Position converter cannot handle transcripts mapped to two locations #341

Open mutalyzerbot opened 8 years ago

mutalyzerbot commented 8 years ago

Original ticket: https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/151 Original date: 2013/10/16 Original reporter: martijn

There are some examples of transcripts that are mapped to two locations, mostly on chromosomes X and Y.

Starting from the genomic location, the position converter works fine, but starting from the transcript, only one of the chromosomes is considered.

mutalyzerbot commented 8 years ago

Original date: 2013/10/16 Original reporter: martijn

Examples can be found with this query:

SELECT
  COUNT( * ) AS aantal,
  GROUP_CONCAT( chromosome ),
  GROUP_CONCAT( gene ),
  transcript,
  version,
  GROUP_CONCAT( protein ) 
FROM  `Mapping` 
GROUP BY transcript, version
HAVING aantal >1;

Example transcripts: NM_001007253, NM_001012288