I am working on Next gen sequenced data. I have used sam tools for the analysis and completed generating variant pileup. Can anyone suggest how to add dbSNP annotations and do cSNP prediction using samtools?? Or can you even suggest any other tool to do this??
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I use a program called annovar. It'll convert vcfs or pileups from samtools and convert them into its own format. It downloads the gene and protein data from UCSC, so you'd have to construct your own data if you were working in an organism that wasn't in their database. I think annovar can probably handle a dbSNP file too. Or Bedtools could intersect your vcf with a .bed file of dbSNP snps.
I work with bacteria, and I cobbled one together by blastxing altered sequence against proteins, and parsing the output.
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