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][1]. Any tips? Thanks in advance!


  [1]: https://github.com/douglasgscofield/snpEffect
Hello,

have a look at [snpEff][1]. Your list of SNP/indel have to be in vcf or bed format.

fin swimmer

  [1]: http://snpeff.sourceforge.net/SnpEff_manual.html