I am working on influenza virus. I would like to annotate variants from virus using annovar. I am facing issue in building the database for virus. I have just 8 genes for the influenza virus and have their refseq id. I tried finding the genome id but I couldn't . So I saved all the 8 gene's fasta sequence in one file and used it for building the database for annovar. The annovar program throws an error saying that I don't have refGene.txt file.
Can I create custom GTF file for influenza virus based on these 8 genes?
Have anyone faced similar issue?
Can you suggest any other variant annotation tool apart from annovar?
Thanks Joe for your suggestions. For example, I am interested in these two strains Influenza A virus (A/California/07/2009(H1N1)) and (A/Texas/50/2012(H3N2). From following link http://www.ncbi.nlm.nih.gov/genome/10290, I have following ids,
I don't have genomes for these two strains. Instead I have segments refseq id. So what are the fields manually I need to capture.