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extract the positions from genome where reads from all the samples have aligned

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  • extract the positions from genome where reads from all the samples have aligned

    I have aligned 454 reads from 8 different individuals to the human reference genome using GS reference mapper and converted this alignment into BAMfile now how can I extract the genome positions where the reads from all the 8 individuals have aligned?
    I have all ready put marker in read name to identify the individual it belongs to.
    Any help will be appreciated

  • #2
    Try BEDTools bamToBed

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