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Abnormal genome plot running GATK4 CNV workflow

xuejiaxuejia CrownbioMember

Hi GATK team,
I am a new user of GATK4 CNV workflow. I can get all the output files from computing steps. They all look fine. However, the read dots are missing in the resulting PNG files. I can only see the axes and labels.
This is the command i used:
java -jar /home/jxue/softwares/GATK4_CNV/gatk4.jar PlotSegmentedCopyRatio -TN -PTN E08055T.ptn.tsv -S E08055T.seg -O . -pre E08055 -LOG -schr

Thanks a lot in advance!



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