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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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mask region #229

Closed Xscut closed 1 month ago

Xscut commented 1 month ago

When I use -call with -rd_use_mask, the masked region will be called as a deletion. How can I prevent the masked region from being called in the results

suvakov commented 1 month ago

Which caller you are using and what bin size?

Xscut commented 1 month ago

Which caller you are using and what bin size?

the command being used is cnvpytor -root xxx.pytor -call 1000 -rd_use_mask

suvakov commented 1 month ago

Use -filter_nan in both the -partition and -call steps:

cnvpytor -root xxx.pytor -partition 1000 -rd_use_mask -filter_nan
cnvpytor -root xxx.pytor -call 1000 -rd_use_mask -filter_nan

However, this is a new feature, so update CNVpytor from the GitHub source:

pip uninstall -y cnvpytor && pip install git+https://github.com/abyzovlab/CNVpytor.git

We would appreciate feedback from you on whether this solves the problem. Thank you for raising this question.

Xscut commented 1 month ago

Use -filter_nan in both the -partition and -call steps:

cnvpytor -root xxx.pytor -partition 1000 -rd_use_mask -filter_nan
cnvpytor -root xxx.pytor -call 1000 -rd_use_mask -filter_nan

However, this is a new feature, so update CNVpytor from the GitHub source:

pip uninstall -y cnvpytor && pip install git+https://github.com/abyzovlab/CNVpytor.git

We would appreciate feedback from you on whether this solves the problem. Thank you for raising this question.

Thank you very much; this problem has been solved successfully.