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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Argument "NA" isn't numeric in numeric gt (>) at ~/detect_cnv.pl line 1632. #80

Open shaoxiong2588 opened 2 years ago

shaoxiong2588 commented 2 years ago

Hi,

I want to know how to deal with this problem :Argument "NA" isn't numeric in numeric gt (>) at ~/detect_cnv.pl line 1632.There are about 3000 lines about this problem There are 1571 individuals of my sample and 48858 SNPs across the pig genome .After I do detect_cnv.pl to find cnv ,the result shows there are 6274 raw_cnv .But after QC by the condition of -qclrrsd 0.30 -numsnp 3 -maxnumsnp 100 --length 10k ,there are only 1745 cnv. When I use CNVRuler to find the overlapping cnvs ,there is zero Could you tell me how can I deal with this

Deng

oshintogla commented 2 years ago

I am facing the same problem: Argument "" isn't numeric in numeric gt (>) at detect_cnv.pl line 1357. And the same argument in many lines has been seen. This problem occurred when I applied SNP QC on my data set (call rate > 98% & maf < 0.05). When I did the analysis on my dataset without any SNP QC, this problem did not happen. Number of CNVs I got after QC was also less.