keep only filtered entries in pytor file

[thedam]

Hey
To obtain a filtered vcf file, I do:

cnvpytor -root rd.pytor -view 1000 <<ENDL
set Q0_range 0 0.5
set pN_range 0 0.1
set size_range 1000 inf
set p_range 0 0.00001
set dG_range 1000 inf
set print_filename output_1k.vcf
print calls
ENDL

But how to persist these changes in rd.pytor file?
I want to remove enteries that are filtered out, because when I want to display "bin 1000" in IGV.js, I get error: Out of Memory

Cheers

[arpanda]

The view mode is primarily used for displaying, filtering, or exporting results; it typically does not modify the pytor file (i.e., deleting records ).

As I understand it, you are trying to view a pytor file using IGV.js and would like to see the filtered calls highlighted in the CNVpytor track.

Currently, this feature is not available in IGV.js's CNVpytor track, but I am actively working on it. I expect to have a development version ready in a few weeks. If you're comfortable using a development version of IGV.js, I’ll keep you updated here.

Regarding the Out of Memory issue, I believe it is related to IGV.js's CNVpytor track. This occurs because the browser is consuming too much memory while attempting to load the entire genome. You might try loading only a few chromosomes instead or increasing the bin size.

-Arijit

[thedam]

As I understand it, you are trying to view a pytor file using IGV.js and would like to see the filtered calls highlighted in the CNVpytor track.

Well, if there would be an option to remove filtered calls from pytor file, it would be fine. I hope, that with less data of bin 1000 in .pytor file would allow to open a .pytor track with bin 1000 in IGV.js.
Bins 10000 and 100000 works fine.

Anyway, thanks for the reply, I can't use development version of IGV.js, as I need a stable production version, however I'm patiently waiting for improvements. Great job, thanks!