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  • [Annovar] Annotate SNPs in Samples

    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

  • #2
    snpEff might be useful

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    • #3
      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.

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