What is " dbSnp132.vcf " in the snpEff tutorial?

Question

[tmrhyd]

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!!

Answer 1

[ATpoint]

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.

[tmrhyd]

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!!! :)

[ATpoint]

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.

[AK]

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.