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Picard CollectHsMetrics PCT_EXC_OFF_TARGET

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    Megan Shand

    Hi,

    The number of excluded off target bases should be PCT_EXC_OFF_TARGET * PF_BASES_ALIGNED. The divisor for calculating all of the PCT_EXC metrics is PF_BASES_ALIGNED.

    Just for clarity, PF stands for passing filter, but it references the vendor filter specifically. So it's reads that pass the sequencer filter, not any other filters.

    Hope that helps!

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    Holly Corbitt

    Thank you for the quick response...

    So these aren't percents of percents (i.e. why do all the PCT_EXC add up to 1 then)? If you did this sort of calculation for all of them then you would get the total number of bases passing filter.

    My other line of evidence is that if you use PCT_EXC_OFF_TARGET * PF_BASES_ALIGNED to get the total number excluded for off target and add that back to the on target bases, you get more than the total bases.

    Here is my example data:

    PF_BASES_ALIGNED 4,915,335,315

    ON_TARGET_BASES 1727103724

    PCT_EXC_BASEQ 0.007394
    PCT_EXC_DUPE 0.069799
    PCT_EXC_MAPQ 0.053678
    PCT_EXC_OFF_TARGET 0.798181
    PCT_EXC_OVERLAP 0.073081

     

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    Megan Shand

    There have been some changes in that section of the code recently. Which version are you using?

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    Holly Corbitt

    Hi Megan,


    Maybe that is the root issue. We are still using v1.14.

    I re-ran it on the new version and the metrics now make sense.

     

    Thanks!

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