This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What is " dbSnp132.vcf " in the snpEff tutorial?

What is " dbSnp132.vcf " in the snpEff tutorial listed below? I have a algae genome and am wondering what this is, and if it is just for human genomes not plant genomes?

Here is the line of code I am trying to use.

java -jar SnpSift.jar annotate dbSnp132.vcf variants.vcf > variants_annotated.vcf

Here is the tutorial I was looking at:

http://snpeff.sourceforge.net/SnpSift.html#annotate

Thank you so much!!

genome assembly snp
• 2,158 views • link
updated by ATpoint ATpoint • written by tmrhyd • tmrhyd

1 answer

dbSNP is a database that stores variant information in human. It can be used to annotate variants. It is not intended for anything but human samples.

• 0 views • link
written by ATpoint ATpoint

So I can't use snpEffs annotation function for algae? What should I use to annotate the VCF file I have?

Thank you so much!!! :)

• 0 views • link
written by tmrhyd • tmrhyd

You can but you'll have to find an appropriate annotation database. I do not work with algae so I am of little help here. Maybe see if Ensembl has something that you can use with its VEP application.

• 0 views • link
written by ATpoint ATpoint

If you'd like to work with your own genome the first step is to build a database for it. Have a look at: Configuring a new genome.

• 0 views • link
written by AK AK

Log in to answer this question.

More posts like this