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mutalyzer / mutalyzer2

HGVS variant nomenclature checker
https://mutalyzer.nl
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Variant Description Extractor error #438

Open jtdendunnen opened 6 years ago

jtdendunnen commented 6 years ago

using the VDE with ReferenceSeq: TCCATCCCAGCGCTCCCAGCTGGAGGCCTATTCCACTCTGCTGGCCAACATGGGCAGTCTGAGCCAGACGCCGGGACACAAGGCTGAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCATCAGCATCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCTCAGCAGGGCTCCGGGGCTCATCACCCCGGGGTCCCCCCCACCAGCCCAGCAGAACCAGTACGTCCACATTTCCAGTTCTCCGCAGAACACCGGCCGCACC and SampleSeq: TCCATCCCAGCGCTCCCAGCTGGAGGCCTATTCCACTCTGCTGGCCAACATGGGCAGTCTGAGCCAGACGCCGGGACACAAGGCTGAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCTCAGCAGGGCTCCGGGGCTCATCACCCCGGGGTCCCCCCCACCAGCCCAGCAGAACCAGTACGTCCACATTTCCAGTTCTCCGCAGAACACCGGCCGCACC

I get a description which is not correct. The sequence GCA[12]TCAGCATCA[1]GCA[14] changes to GCA[43]. Please check what goes wrong.

jkvis commented 6 years ago

According to mutalyzer the description is [127T>G;133T>G]. This is indeed incorrect. Running the VDE locally gives me:

0--126, 0--126, 1, 0, 0--0
126--127, 126--127, 4, 5, 0--0
127--132, 127--132, 1, 0, 0--0
132--133, 132--174, 9, 5, 135--177
132--133, 174--175, 20, 1, 0--0
133--280, 175--322, 1, 0, 0--0

The variants indicated with type 9 and type 20 seem to be missing (this is a transposition structure). Probably something that is not yet covered in describe.py. We should look into that.