AlphaMissense Plugin VEP

Question

[Andrea]

I've installed alphamissense plugin in VEP, but I can't use it. I've downloaded the requested files and launch the tabix command before use it.

Then I've launched the command but I got this error:

WARNING: Failed to instantiate plugin AlphaMissense:
  ERROR: No file specified
Try using 'file=path/to/file.tsv.gz'

The command is:

./vep -i Sample1.hard-filtered.vcf.gz -o Test.txt --cache /home/aghiroldi/ensembl-vep/ --plugin Blosum62 --plugin AlphaMissense,AlphaMissense_hg19.tsv.gz.tbi --everything --offline --assembly GRCh37 --tab

Probably I'm wronging in indicating the file.

Thanks

[Ram]

EDIT: See GenoMax's comment below, you need what they specify.

You're specifying the index file name. Try specifying the full path to the tsv.gz file instead like so: --plugin AlphaMissense,/absolute/path/to/AlphaMissense_hg19.tsv.gz

[GenoMax]

Looks like the software actually wants you to put the word file in the command.

--plugin AlphaMissense,file=/absolute/path/to/AlphaMissense_hg19.tsv.gz

[Miguel]

surprisingly I have problems with REVEL plugin with parsing "file" word in this context, when I remove it and simply type the path it works. I think it is prob related with VEP version?

[Ram]

That's a good catch - definitely worth a bug report.

[Ram]

Thank you, I missed that. I went with VEP's regular plugin specification format.