text: user2693: 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?
  
  user2714: I recently used SIFT4G to predict the deleteriousness for a SNP dataset in Arabidopsis. 
  I noticed that besides this, the tool also provides annotation for the SNPs (like gene region, amino acid substitution, start/stop etc.)
  They have an Arabidopsis database readily available so you don't have to generate your own. Your input should be enough to run the tool, although you might have to do some reformatting (the tool requires VCF format files).
  One thing though, not all SNPs are considered by the tool. Intronic SNPs and SNPs outside gene regions are ignored afaik.
  
  user6500: 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
  
original_text: 2693: <p>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).</p>
  
  <pre><code>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
  </code></pre>
  
  <p>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 <em>boom</em>, annotation. But I couldn't find any, except maybe <a href="https://github.com/douglasgscofield/snpEffect" rel="nofollow noreferrer">snpEffect</a>. Any tips?</p>
   2714: <p>I recently used <a href="http://sift.bii.a-star.edu.sg/sift4g/AnnotateVariants.html" rel="nofollow noreferrer">SIFT4G</a> to predict the deleteriousness for a SNP dataset in Arabidopsis. </p>
  
  <p>I noticed that besides this, the tool also provides annotation for the SNPs (like gene region, amino acid substitution, start/stop etc.)</p>
  
  <p>They have an Arabidopsis database readily available so you don't have to generate your own. Your input should be enough to run the tool, although you might have to do some reformatting (the tool requires VCF format files).</p>
  
  <p>One thing though, not all SNPs are considered by the tool. Intronic SNPs and SNPs outside gene regions are ignored afaik.</p>
   6500: <p>The Ensembl Variant Effect Predictor will annotate your A. thaliana variants:
  <a href="http://plants.ensembl.org/Oryza_sativa/Tools/VEP" rel="nofollow noreferrer">http://plants.ensembl.org/Oryza_sativa/Tools/VEP</a></p>
  
  <p>The web based tool will use the reference genome assembly and gene annotation used in the Ensembl browser:
  <a href="http://plants.ensembl.org/Arabidopsis_thaliana/Info/Annotation/#assembly" rel="nofollow noreferrer">http://plants.ensembl.org/Arabidopsis_thaliana/Info/Annotation/#assembly</a></p>
  
  <p>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.</p>
  
  <p>You can find all of the documentation here:
  <a href="http://www.ensembl.org/info/index.html" rel="nofollow noreferrer">http://www.ensembl.org/info/index.html</a></p>
  
  <p>Best wishes</p>
  
  <p>Ben
  Ensembl Helpdesk</p>
  