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Ensembl / VEP_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)
Apache License 2.0
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mutfunc: Skip annotation if no sequence #728

Closed nakib103 closed 3 months ago

nakib103 commented 4 months ago

The mutfunc plugin needs translation sequence for annotation. The VEP cache do not have the translation sequence. So, when --offline is used without a FASTA mutfunc do not annotate anything. Added a warning and skip any annotation logic altogether for such case.

Test

vep -i <repo_dir>/ensembl-vep/examples/homo_sapiens_GRCh38.vcf --cache <cache_dir> --cache_version 112 -a GRCh38 --force --plugin mutfunc,db=<plugin data_dir>/mutfunc_data.db --offline