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  • Lessthan3
    Junior Member
    • Jul 2012
    • 2

    #1

    BioInformatics beginner..# of reads aligned to a genome using GATK

    I was recommended to use this website for information, but I cannot find a lot of information on GATK here.
    I need to find the # of reads aligned to a genome. How would I go about doing that in java? This is to assess the quality of sequencing data in BAM files. I am not very familiar with any methods or implementation of it, which I cannot find on the GATK wiki. I understand that there are data traversals and data walkers, but how do I use them? Some example code in which a walker is used would be really helpful.

    Thanks

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