AlphaMissense Plugin VEP
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6 months ago
Andrea ▴ 10

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

Plugin VEP Alphamissense • 1.3k views
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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

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2
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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
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1
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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?

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

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

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