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basequality filter for sambamba depth region/window? #154
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Hi Martin, I've added (minimum) base quality filtering for all modes. |
Thanks! |
Hi Artem, I did some small test, and I am afraid the -q option is not working properly (at least not the way I expected it to do ;) ). It appears that the q filtering is fixed on base 2 only (irrespective of orientation of the read) and when this base does not meet the threshold, the entire reads (thus all bases) are removed from the analysis. The way I see the filtering is that each base in a read thats lower than the quality is removed, the remaining bases should be used. Let me know if you need more input (or test files)! Greetz |
Oops, you are right. Thanks for the testing. |
OK, I made the changes so that now bases are counted according to your suggestion. A read is counted only if it has at least one good quality base in the region. Indels are just ignored. |
Hi Artem,
Is it possible to filter on basequality for sambamba depth region/window?
I see the option -p for depth base but not for region/window.
Also, I can not find basequality in the code for the filter (-F) option.
Did I miss it, or is it not possible (yet)?
Btw. the tool is working great! Keep up the good work!
Greetz,
Martin
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