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  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #1

    idxstats option for samtools

    I searched for previous posts on this but the question below was not explicitly answered in the three threads I found.

    So here goes:

    The output from the "idxstats" command in samtools generates four values. What exactly does the last column (# unmapped reads) signify?

    Is "idxstats" the best way to "count" mapped reads in BAM files?

    Thanks in advance.

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