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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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How to interpret merged_calls result from command line #214

Closed NannapatS closed 6 months ago

NannapatS commented 6 months ago

Hi I used command line on HPC as below for trio sample. cnvpytor -root proban1.pytor father1.pytor mother1.pytor -view 100000 set Q0_range -1 0.5
set p_range 0 0.0001
set p_N 0 0.5
set size_range 50000 inf
set dG_range 100000 inf
set print_filename mergedtrio1view100000annotatemerge.tsv set annotate
print merged_calls
quit

Then I got result as below Capture

My question are

  1. I think data on column D, E and F that are copy number, doesn't I.
  2. What does the values on column G? Please help me, thank a lot anyone in advance.
arpanda commented 6 months ago

You are correct. The columns D, E, and F correspond to the copy number of your samples, while column G indicates the index of the sample where CNV is called.

In Row 2, a CNV call is identified for samples 1 and 2, but not for sample 0. In Row 3, the region's coordinates differ from those in Row 2, and it is identified as a CNV solely in sample 0.