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BAM records filtering based on flag ? #16

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af8 opened this issue Jan 24, 2021 · 4 comments
Closed

BAM records filtering based on flag ? #16

af8 opened this issue Jan 24, 2021 · 4 comments

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@af8
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af8 commented Jan 24, 2021

Hi,

Is it possible to select bam records used for d4 file calculations based on bam flag value (as it is done in mosdepth with --flag 1796) ?

And if not possible at this time, are duplicates included or excluded from d4 create command ?

Thanks
Anthony
@arq5x
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arq5x commented Feb 16, 2021

@38 this would be a very helpful feature to add. Can you tackle it when you have a chance?

@af8
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af8 commented Mar 3, 2021

@38 I was also thinking that incorporating a threshold on MapQ could be very useful as well.
Many thanks

@af8
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af8 commented Mar 3, 2021

Sorry just realized this mapq option actually exists :-)

@arq5x
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arq5x commented Aug 18, 2021

@38 can you close this issue?

@38 38 closed this as completed Aug 19, 2021
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@arq5x @38 @af8