SNP/indel annotation in Arabidopsis

Question

[Federico Giorgi]

Hi all,

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? Thanks in advance!

Answer 1

[finswimmer]

Hello,

have a look at snpEff. Your list of SNP/indel have to be in vcf or bed format.

fin swimmer

[Tm]

Yes snpEff is a good tool. I have used snpEff and have got satisfactory results. It takes annotation file (.gtf) and .vcf file of variants as input.