You could use SNPdat (http://code.google.com/p/snpdat). Its available from BMC bioinformatics
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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.
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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
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variant annotation
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?Tags: None
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