Entering edit mode
3.9 years ago
tmrhyd • 0
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:
Thank you so much!!
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!!! :)
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.
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.