Cnvnator Genotype Regions Error : Can'T Find Bin 1000

Question

[William]

I used CNVNator to call CNV in multiple samples and I am now using the same tool to genotype these CNV calls in all the samples.

This is how I created the cnv calls.

mkdir mySample1
#extract reads from bam to root file
/opt/CNVnator_v0.2.7/bin/cnvnator -root mySample1/mySample1.root -tree /data/bam/mySample1_dedup_realigned.bam > mySample1/mySample1_extract.out
#create histograms
/opt/CNVnator_v0.2.7/bin/cnvnator -root mySample1/mySample1.root -his 100 -d /data/splitFastaFiles/ > mySample1/mySample1_histogram.out
#calculate statistics
/opt/CNVnator_v0.2.7/bin/cnvnator -root mySample1/mySample1.root -stat 100 > mySample1/mySample1_stats.out
#rd signal partitioning
/opt/CNVnator_v0.2.7/bin/cnvnator -root mySample1/mySample1.root -partition 100  > mySample1/mySample1_partition.out
#cnv calling
/opt/CNVnator_v0.2.7/bin/cnvnator -root mySample1/mySample1.root -call 100 > mySample1/mySample1_calls.out

This is how I am genotyping an region from the mySample1_calls.out file.

opt/CNVnator_v0.2.7/bin/cnvnator -root mySample1/mySample1.root  -genotype 100
chr1:47665301-47665700

This is the output / error I get:

Can't find directory 'bin_1000'.
Can't find directory 'bin_1000'.
Genotype chr1:47665301-47665700 ACI.root 0.345314 -1

The output looks correct in IGV but I have no idea were the error

Can't find directory 'bin_1000'.

comes from since I didn't use a bin size of 1000 anywhere. Can I just safely ignore this "error" or is there anything I can do to solve it?

[izwanspp]

Did you try repeating the entire process (-his, -stat, -partition, -call) using a bin size of 1000 instead of 100? It worked for me.

Answer 1

[cyrielle]

A Docker container for human CNV calling with CNVnator was recently developed. All you need to do is download the container and and make sure you have a WGS .bam. Calling then starts automatically, so no need to compile and run the software yourself. More info is available in this blogpost goo.gl/uodlUO

Answer 2

[Alicia B]

Hi William... Did you ever figure out what was going on here? or if this error message mattered? I am following the same steps as you as and am also getting this error message.

Also you mention that you were viewing your output in IGV. What format did you convert your cnvnator output to? Was it VCF? I'm trying to find a good way of inputting all my CNVs in IGV to compare to ref genome and annotations...

Thanks for your help!

[William]

Nope .... sorry.