search

rpetit3 / vcf-annotator

Add biological annotations to variants in a given VCF file.
MIT License
26 stars 7 forks source link

Is there an alternative way to do the annotation without the GenBank file? #7

Closed vappiah closed 3 years ago

vappiah commented 3 years ago

Hello developer(s). I would like to use vcf-annotator on my plasmodium snp data. However there seems to be no genebank file available from the download site for the reference genome https://plasmodb.org/plasmo/app/downloads/release-49/Pfalciparum3D7/)

Is there an alternative way to do the annotation without the genebank file? Please advice

rpetit3 commented 3 years ago

If its the same genome as this one Plasmodium falciparum 3D7 (malaria parasite P. falciparum), then the GenBank file can be found here: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/765/GCF_000002765.5_GCA_000002765/GCF_000002765.5_GCA_000002765_genomic.gbff.gz

Be warned though, I've only tested vcf-annotator on prokaryotic genomes. I think it should work for you, but it might be slow.

vappiah commented 3 years ago

Thanks @rpetit3 . I will try with the file

rpetit3 commented 3 years ago

Great! Hope it works for you! If not please feel free to reopen this issue