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Molmed / checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
http://checkqc.readthedocs.io/
GNU General Public License v3.0
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Detect index switch + reverse complemented index #86

Open matrulda opened 5 years ago

matrulda commented 5 years ago

I encountered a case where CheckQC couldn't tell the whole story behind incorrectly specified indexes:

Index in sample sheet: 

ACATAGCG+CTAGCTTG

Index found in undetermined indexes: 

CAAGCTAG+ACATAGCG

Reported by CheckQC: 

Index: CAAGCTAG+ACATAGCG on lane: 1 was significantly overrepresented (5.9%) at significance threshold of: 1%.
We found a possible match for the reverse complement of tag: CAAGCTAG, on: Lane: 1, for sample: Sample_A
The tag we found was: CTAGCTTG.
This originated from the dual index tag: CAAGCTAG+ACATAGCG

It would have been helpful if it also was reported that ACATAGCG was find among index 1 in the sample sheet.