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butkiem / COCOS

COCOS: Codon Consequence Scanner for annotating reading frame changes induced by stop-lost and frame-shift variants
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Unable to produce expected output cocos.fasta #1

Open huimingx opened 4 years ago

huimingx commented 4 years ago

Hi,

I'm trying to use the COCOS plugin with vep (version 95) and it doesn't seem to be producing the cocos.fasta file that is expected when successful. No vep errors or relevant warnings appeared either. The resulting output does have COCOS relevant headers but no annotation for the variant entries. Is this plugin only compatible with certain vep versions? My test command is as following:

/usr/bin/perl -I ./vepCache/Plugins/ /usr/bin/variant_effect_predictor.pl --dir ./inputs/VEP_cache --vcf -i ./example/example.vcf --cache --offline --force_overwrite --plugin cocos,"./cocos.fasta"

Thanks!

Lovatiana-omic commented 2 years ago

Hi, I got the same issue. I have no output file for COCOS. I tried with the example.vcf

/home/lovatiana/ensembl-vep/vep -i ./example.vcf --cache --port 3337 --refseq --force_overwrite --dir_plugins /home/lovatiana/ensembl-vep/cocos-github/ --plugin cocos,"./example_output.fasta"

Thanks for helping!