Generate SNP/indel annotation in Arabidopsis I have a genome-wide list of germline SNPs and short indels for Arabidopsis thaliana, which I generated with Varscan. Regardless of the tool used to generate them, I would like to annotate them, i.e. knowing which ones can cause an aminoacid change or an early stop, using the default Arabidopsis thaliana Columbia 0 cultivar, for which I have both the sequence (FASTA from TAIR10) and the updated annotation (GFF from Araport).

Chrom   Position    Ref Var
Chr1    626503  G   T
Chr1    926694  C   T
Chr1    5280350 C   A
Chr1    5699993 C   A
Chr1    7004559 G   A
Chr1    8325810 C   T
Chr1    9371723 T   G


What I want to do is similar to what Annovar does, but unfortunately Annovar does not support Arabidopsis. I was thinking of an already existing R pipeline that takes in a genome, an annotation, a SNP/indel list and boom, annotation. But I couldn't find any, except maybe snpEffect. Any tips?
The Ensembl Variant Effect Predictor will annotate your A. thaliana variants:
http://plants.ensembl.org/Oryza_sativa/Tools/VEP

The web based tool will use the reference genome assembly and gene annotation used in the Ensembl browser:
http://plants.ensembl.org/Arabidopsis_thaliana/Info/Annotation/#assembly

However, if you use the command-line version of VEP, you can provide your own reference genome assembly and gene annotation files to be used as a reference.

You can find all of the documentation here:
http://www.ensembl.org/info/index.html

Best wishes

Ben
Ensembl Helpdesk