variant annotation

[Balat]

Hi,
Most of the tools related to variant annotations seem to be related to humans. I work on a plant species where we only have the draft genome and not annotated yet. I have done an rna-seq experiment and I have found several snps using samtools. I got a gtf file by aligning reads against the genome sequence with bowtie and tophat. The gtf file only has transcirpt information and no orf or CDS information. Does any one have a script which takes the positions of the snps, annotations from a gtf file and the genome sequence in fasta format and predict if the snps are synonymous or non-synonymous?

[SDBP]

Hi,
I am too am facing this problem.
I am working on a bacterial genome. I have the Genome sequence, the gene annotations gff file and and list of variations (not annotated).

How do I annotate the variants using the gff file and the genome sequence file, to map the variants to genes.

Any ideas how to go about?
tx,
Durga

[Balat]

Hi Durga,
I use a script in 'popoolation' (http://code.google.com/p/popoolation/) package to annotate the variants. You need to supply a pileup file and a gtf file with CDS to annotate the variants.

[d1antho]

You could use SNPdat (http://code.google.com/p/snpdat). Its available from BMC bioinformatics

http://www.biomedcentral.com/1471-2105/14/45