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validation: Exome Sequencing data

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  • validation: Exome Sequencing data

    HI all,
    I have 10 pairs of normal-tumor whole exome data. The mutation calling has been performed and many interesting SNVs were detected. Allele Frequency cutoff 0.05 was used.

    However, our funding on this project is limited and it is unlikely to validate a large number of SNVs.

    We know that there are false positives in the obtained SNVs. I am thinking to use another tool to call the SNVs and use the common SNVs detected by both tools as the "true" SNVs. Then we can go ahead to calculate the mutation spectrum, mutually exclusivity ect.

    Here I am trying my luck to see if there is a better idea to get a relatively robust list of SNVs.

    Any input will be appreciated.

    Thank you.

  • #2
    http://www.biomedcentral.com/1471-2105/14/189

    Comparing somatic mutation-callers: beyond Venn diagrams
    Su Yeon Kim and Terence P Speed
    BMC Bioinformatics 2013, 14:189 doi:10.1186/1471-2105-14-189

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