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  • Diversity from bam files

    Hi All,

    I was wondering whether anyone had any advice on the best way to calculate estimates of diversity from a bam file. It's a virus, so I'm modelling one bam file as if I'd merged several to form a sequence representing the population. I am thinking that theta might be the best measure to use - does anyone have any favourite tool for doing this?
    I've tried pileup in samtools using bcftools /dev/null to get an estimate but all I've ended up with is theta = nan!!

    Any help would be greatly appreciated.

    All the best,

    kat

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