SNP annotation of A VCF file

Question

[mrnjeri]

I have a VCF file derived from mapping RNA-Seq reads to a denovo assembled reference. I used samtools mpileup and bcftools to derive the VCF file. The study species have no genome. please guide on how to annotate SNPs?

[Matthieu Miossec]

Could you clarify what you mean when you say the study species have no genome?

[WouterDeCoster]

What kind of annotation do you have in mind? Which information would you like to add? What is the purpose of your study? Adding more information will get you quicker to a reply which is useful for you, don't make use make guesses on what you exactly want.

[mrnjeri]

SNP annotation from denovo assembled reference. How can I successful do that using this information available. I would also like to know how to convert vcf file to a binary data matrix

[DG]

You should move this to be a comment (Add comment under your question or add reply to WouterDeCoster's comment) instead of submitting updates as an answer to your question. It will make things easier to follow in terms of details of your question and the answers to it. Thanks

[mrnjeri]

Thanks for the advices

Answer 1

[Denise CS]

If you have a FASTA file for the sequences of your species plus its GTF file (containing some annotation of genes and other features), you can try to build a cache and run the Ensembl VEP. Send an email to the Ensembl helpdesk with additional info and/or if you get stuck.

[mrnjeri]

Thanks a lot. It does not have any GTF file. Kindly help