Question: SNP annotation of A VCF file
0
gravatar for mrnjeri
3.7 years ago by
mrnjeri0
mrnjeri0 wrote:

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?

snp forum • 1.8k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by mrnjeri0

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

ADD REPLYlink written 3.7 years ago by Matt Miossec320

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.

ADD REPLYlink written 3.7 years ago by WouterDeCoster42k

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

ADD REPLYlink modified 3.6 years ago • written 3.7 years ago by mrnjeri0

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

ADD REPLYlink written 3.7 years ago by DG7.1k

Thanks for the advices

ADD REPLYlink written 3.7 years ago by mrnjeri0
0
gravatar for Denise - Open Targets
3.7 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.1k wrote:

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.

ADD COMMENTlink written 3.7 years ago by Denise - Open Targets5.1k

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

ADD REPLYlink written 3.7 years ago by mrnjeri0
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