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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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deletion event is wrongly assigned as duplication #193

Open fsnibs10 opened 1 year ago

fsnibs10 commented 1 year ago

Hi authors,

I can run cnvpytor successfully for one strain, but there is an unexpected result for I: 24001-25000.

deletion I:23001-24000 1000 0.0000 8.787960e-05 3.130581e-47 1.000000e+00 1.000000e+00 -1.0000 0.0000 23100 duplication I:24001-25000 1000 0.0024 1.829800e-04 5.074086e-46 1.000000e+00 1.000000e+00 1.0000 0.0000 24100 deletion I:28001-31400 3400 0.2016 4.722641e-04 3.077144e-12 1.816500e-01 7.963554e-43 0.7610 0.0294 28100

After observing IGV mapping, there should be a deletion event here. I don''t know why cnvpytor reports "duplication".

image

suvakov commented 1 year ago

Strange. Can you share .pytor file with me? My email is suvakov at gmail. Thanks

fsnibs10 commented 11 months ago

Hi suvakov,

I sended you an email and attached the pytor files. Thanks for your help!

xiucz commented 11 months ago

Hi, @suvakov I am facing the same issue as well. Can you please take a look at it? Thank you very much!

chr4    141300001   CNVpytor_dup43  .   <DUP>   .   PASS    END=141700000;IMPRECISE;SVLEN=400000;SVTYPE=DUP;pytorRD=0.014548899371722972;pytorP1=0.0028498760122910856;pytorP2=43163869.60494417;pytorP3=0.0028498760122910856;pytorP4=43163869.60494417;pytorQ0=0.0;pytorPN=0.0;pytorDG=49344400.0;pytorCL=rd_mean_shift   GT:CN   0/1:2
chr16   87340001    CNVpytor_dup330 .   <DUP>   .   PASS    END=87530000;IMPRECISE;SVLEN=190000;SVTYPE=DUP;pytorRD=0.003495592688214326;pytorP1=0.0;pytorP2=13.1378512006949;pytorP3=0.0;pytorP4=13.1378512006949;pytorQ0=0.0;pytorPN=0.0;pytorDG=859500.0;pytorCL=rd_mean_shift    GT:CN   0/1:2
chr17   29330001    CNVpytor_dup336 .   <DUP>   .   PASS    END=29680000;IMPRECISE;SVLEN=350000;SVTYPE=DUP;pytorRD=0.0018806006708567012;pytorP1=0.0;pytorP2=1.2683364206343739e-06;pytorP3=0.0;pytorP4=1.2683364206343739e-06;pytorQ0=0.0;pytorPN=0.0;pytorDG=4067100.0;pytorCL=rd_mean_shift  GT:CN   0/1:2
chr17   33040001    CNVpytor_dup339 .   <DUP>   .   PASS    END=33150000;IMPRECISE;SVLEN=110000;SVTYPE=DUP;pytorRD=0.005576928461336835;pytorP1=0.0;pytorP2=43244.56668226278;pytorP3=0.0;pytorP4=43244.56668226278;pytorQ0=0.0;pytorPN=0.0;pytorDG=1526000.0;pytorCL=rd_mean_shift GT:CN   0/1:2

Best, xiucz