Bug in plotrdbaf.py - Githubissues

abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

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Bug in plotrdbaf.py #188

Closed gevro closed 4 years ago

gevro commented 4 years ago

Hi, I'm getting this error: root@a1a1ae2b281d:/home/dnanexus# /home/dnanexus/CNVnator/plotrdbaf.py -bs 50000 -rdbs 50000 -o /home/dnanexus/in/plotrdbaf.pdf -t chr22 /home/dnanexus/in/UDP-2501_genome.cnvnator.chr22.root chr22:1-50818468 Traceback (most recent call last): File "/home/dnanexus/CNVnator/plotrdbaf.py", line 40, in for e in t: TypeError: 'TObject' object is not iterable

Seems like a bug. The root file otherwise works fine for everything else.

gevro commented 4 years ago

I found the problem. plotrdbaf.py only works when there is annotated vcf data in the root file. This should be clarified in the documentation.

suvakov commented 4 years ago

Thanks

yeroslaviz commented 3 years ago

How did you solve it?

what is an annotated vcf file in this case?

thanks