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Somatic mutation profiling from 454 tumor-normal paired data

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  • Somatic mutation profiling from 454 tumor-normal paired data

    Hello All,

    I would be interested to do somatic mutation discovery from 454 tumor-normal paired data. Since I have handled many projects on Illumina and SOLiD project on the same requirements, but want to streamline the pipeline for 454, as the longer reads should be perfectly aligned and variants called with less false positives. I have seen BWA-sw+samtools+varscan/somaticsnipper/Joint-snvmix is one approach. But I would like to know from all what's your suggestion(s) on this. (Unfortunately I dont have access to GS Mapper s/w otherwise it would have been a nice option for mapping)

    Best,

    Praveen.
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