AlphaMissense Plugin VEP
0
0
Entering edit mode
13 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 • 1.8k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode

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
ADD REPLY
1
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2058 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6