Hi again Alec,
Maybe I wasn't clear before.
If there are, for example, 32% bases in the target covered at 2x (i.e.
non-zero coverage), then I would expect that the fold 80 base penalty
returned a fold related to 80% of those original 32% of bases. Therefore
the actual percentage of covered bases in the target should not matter.
Thank you for your thoughts.
Esteban
El martes, 27 de mayo de 2014, Esteban Czwan <[email protected]> escribió:
> Hi Alec,
>
> Thank you for your answer.
>
> I am afraid I cannot fully understand your comments. Here's the definition
> of the fold 80 base penalty from Picard:
>
> FOLD_80_BASE_PENALTY: The fold over-coverage necessary to raise 80% of
> bases in "non-zero-cvg" targets to the mean coverage level in those targets.
>
> According to the definition it is not required that more than 80% of the
> bases in the target should have coverage.
>
> What I understand is that the fold 80 base penalty is the fold
> over-coverage needed to raise 80% of bases in covered targets to the mean
> coverage. As far as I see it, it should not matter how many bases are
> actually covered in the target.
>
> What do you think?
>
> Thank you all once again.
>
> Best wishes,
>
> Esteban
>
> El martes, 27 de mayo de 2014, Alec Wysoker <[email protected]>
> escribió:
>
>> Hi Esteban,
>>
>> Less than 80% of the bases in targets that have non-zero coverage have
>> any coverage at all. The program can't know how many times more sequencing
>> would be required to raise 80% of bases to mean coverage, so it returns
>> infinity.
>>
>> -Alec
>>
>> On May 27, 2014, at 5:54 AM, Esteban Czwan <[email protected]> wrote:
>>
>> > Dear all,
>> >
>> > I calculated Picard HsMetrics and the FOLD_80_BASE_PENALTY metric had
>> > a question mark ("?").
>> >
>> > I have attached the output file to this email.
>> >
>> > Do you know what might have happened?
>> >
>> > Thank you and best wishes,
>> >
>> > Esteban
>> >
>> <EXOMEV3_KAPA_1_microgram_subsample_calculate_hs_metrics.txt>------------------------------------------------------------------------------
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