Get REVEL plugin started with VEP

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3.3 years ago

Filago ▴ 100

Hello, I am using the VEP tool (version 104) and already managed to annotate a VCF-file (hg19) with basic annotations and CADD. Furthermore I wanted to annotate it with the REVEL plugin. So I downloaded the plugin, as well as the data for REVEL (and preprocessed it according to the information given at the vep website https://m.ensembl.org/info/docs/tools/vep/script/vep_plugins.html).

The following error occurs now when running VEP:

Use of uninitialized value $assembly in hash element at /.vep/Plugins/REVEL.pm line 112. 
Use of uninitialized value in string eq at /home/username/.vep/Plugins/REVEL.pm line 112.

and here is the "REVEL-part" of my vep command:

--plugin REVEL,/home/username/.vep/Plugins/new_tabbed_revel.tsv.gz

and here is the header of the REVEL file after preprocessing it:

#chr    hg19_pos        grch38_pos      ref     alt     aaref   aaalt   REVEL   Ensembl_transcriptid

Coud someone tell me please how to solve this issue?

Many thanks in advance!

Andreas

VCF REVEL VEP • 2.7k views

ADD COMMENT • link updated 3.3 years ago by 2c98a9f9 • 0 • written 3.3 years ago by Filago ▴ 100

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Did you figure out how to solve this?

ADD REPLY • link 3.3 years ago by williamsbrian5064 ▴ 530

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Not yet. Do you have the same problem? Best, Andreas

ADD REPLY • link 3.3 years ago by Filago ▴ 100

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Have you tried specifying the assembly ('--assembly') in the vep command?

ADD REPLY • link 3.3 years ago by 2c98a9f9 • 0

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