[Annovar] Annotate SNPs in Samples

[Coryza]

Hi All,

I want to annotate the SNPs in my data samples via Annovar. But there are so many databases, and parameters, that I'm a little bit lost. Everyone seems to use a different approach, database and so ever. Does anyone know what should be the most optimal steps for me?

My data consists of multiple human cDNA samples of Illumina Paired-End reads from tumor samples. I've mapped this data via Bowtie2, and only extracted the discordant and concordant pairs. I already did the steps; Samtools view, Samtools sort, Samtools rmdup, Samtools mpileup | bcftools view. So I now have different .vcf files which I want to annotate the SNPs of.

I'm particular interested in finding the SNPs in my samples that cause known gene defects (TP53 and all kinds of oncogenes).

- Y

[mmmm]

snpEff might be useful

http://snpeff.sourceforge.net/

[Coryza]

Thanks! I used that and identified all the known SNPs that were in my sample from the dbSnp database. Do you have any ideas of how many known SNP's I can expect in a SKBR3 cell line? I found approximately 1832.