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genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API
MIT License
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Update test file #182

Closed leexgh closed 2 years ago

leexgh commented 2 years ago

Fix: https://github.com/genome-nexus/genome-nexus/issues/529 https://github.com/genome-nexus/genome-nexus/issues/529#issuecomment-919430830

leexgh commented 2 years ago

Test is failing but shouldn't be related

leexgh commented 2 years ago

minimal_example.in.txt test is failing:

-EGFR   1956        GRCh37  7   55242468    55242486    +   protein_altering_variant    In_Frame_Del    DEL ATTAAGAGAAGCAACATCT AGCAA   GCAA                                                                                                ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln    p.L747_S752delinsQ  ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA    19/28   SUCCESS
+               7   55242467    55242486                    AATTAAGAGAAGCAACATCT    AGCAA

This test case was added by https://github.com/genome-nexus/genome-nexus-annotation-pipeline/pull/113 Seems it is added for some VCF -> MAF conversion issue

leexgh commented 2 years ago

File another ticket for fenomic location + annotation validating issue: https://github.com/genome-nexus/genome-nexus/issues/550