vep plugin doesnt tag lof variants

konradjk / loftee

MIT License

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vep plugin doesnt tag lof variants #103

Open roofya opened 1 year ago

roofya commented 1 year ago

Dear loftee

Im applying vep pluggin singularity run --bind $PWD --pwd $PWD /programs/ensembl-vep-110.1/vep.sif vep --plugin LoFtool -i myinput.vcf -o myoutput --fork 8 -gff Homo_sapiens.GRCh38.108.sorted.gff3.gz -fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa --stats_text --stats_file mysummary.txt

but myoutput file doesnt tag or flag lof variants. Please advise

Thank you

boutrys commented 11 months ago

Same problem, all anotation from VEP and other plugins worked, but LOFTEE do not seems to annotate with LoF, and no errors..