Handling deletion in alt protein sequence

Ensembl / VEP_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)

Apache License 2.0

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Handling deletion in alt protein sequence #691

Closed likhitha-surapaneni closed 4 months ago

likhitha-surapaneni commented 4 months ago

ENSVAR-5920

Testing

vep -i input --shift_hgvs 0 --force_overwrite --assembly GRCh37 --database  --hgvs --plugin ProteinSeqs,output.reference.fa,output.mutated.fa

Input

1   955552  .   CATG    C
1   990358  .   ATGA    A
1   990360  .   GA  G
1   990361  .   GA  G
2   217498305   .   T   TGCTGCC
4   40434704    .   AGCGGCTGCGGCGGCTGCGGCC  A
6   41754573    .   C   CCTT
6   43250725    .   GGAA    G

likhitha-surapaneni commented 4 months ago

Hi @nuno-agostinho , I updated the examples to test start_lost, stop_lost. Please let me know what you think about the outputs.

nuno-agostinho commented 4 months ago

Merged to main and postreleasefix/112.