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  • how to identify SNPs and indels between two samples

    I am new to NGS data analysis. I got two individual samples, each sequenced and mapped against the same reference genome.
    Now I want to identify SNPs and short indels between the two samples. What software/pipelines should I use?

  • #2
    Look up "GATK" on your favorite search engine.

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    • #3
      Hi pandafengye,

      you can also samtools mpileup
      &/ or followed by VarScan.

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      • #4
        after you have the variant call file (VCF) upload it to gene-talk.de and filter for snps, indels, etc...
        Analyze Human Sequence Variants
        www.gene-talk.de

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