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niuhuifei / popoolation

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Pi biased by read coverage? #9

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hello,

Is it possible to remove genomic regions from analysis when using 
Variance-sliding.pl based upon read coverage within the window? I am worried 
that Variance-sliding.pl calculations show low values of Pi, Theta, or D, when 
in fact there is just low read coverage in the specified region. Is there a way 
to correct these statistics with percentage of the window that is covered by 
reads, or remove these regions from the analysis altogether?

Any discussion of how read coverage within a window will effect these 
statistics, or can inform window length, would be greatly appreciated.

Many thanks,

Kevin

Original issue reported on code.google.com by kcde...@gmail.com on 18 Sep 2013 at 6:18

GoogleCodeExporter commented 9 years ago 
Hi Kevin,
you can subsample to an uniform coverage, there is the script subsample 
coverage. This also removes regions with a coverage lower than the targeted 
coverage
cheers ro

Original comment by RoKof...@gmail.com on 5 Mar 2014 at 10:01