Any way to set coverage histogram max value

[Stephen Smith]

Hi,

When i run multi bamqc my output coverage histogram is 0-~9000x

Is there a way to limit this to 0-50x as that's where the vast majority of my reads lie?

Thanks,

Stephen

[Konstantin Okonechnikov]

Hi,

By default max coverage is selected in "Coverage histogram", would it be suitable to control it manually?

In the latest release build there is now option available for BAM QC that allows to control maximum limit for targeted coverage:

-cl,--cov-hist-lim <arg>             Upstream limit for targeted per-bin coverage histogram (default is 50X)

This could be included into multi bamqc as an additional option in a similar manner. 

Best regards,

   Konstantin

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[Stephen Smith]

Hi,

Just coming back to this as I've found myself using qualimap again, this time on even more samples.

It would be useful to control the coverage histogram parameters in mutli-bamqc as now I have Coverage Histogram (0 - 125429X), when my read depth should  be in the region of 0-50x.

The output plots are pretty meaningless with this huge x-axis limit.