Question: Cnvnator Run Time
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gravatar for Vivek
7.1 years ago by
Vivek2.3k
Denmark
Vivek2.3k wrote:

Hi,

If anyone has run CNVnator before for cnv detection can you give me an idea of the approximate run time for the steps?

I'm trying to run the histogram generation step with a histogram size of 100bp and its been running without any result for close to 6 hours.

I'm using the following command to generate histograms:

./cnvnator -root chr22.root -chrom 22 -d human_reference/ -his 100

I tried increasing the bin size, downloading an older version, checking on different chromosomes and nothing seems to be helping this case.

I have the same issues on the 1000 genomes bam files when I tried to check with those.

It also prints "Making directory bin_100" but I don't see this in the working directory.

If anyone can share their experience with this tool, it will be helpful!

exome cnv • 2.5k views
ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by Vivek2.3k

To update this, I had initially tried compiling root and cnvnator for red hat linux without much luck and since I have also done the same for Mac OS X and see the same issues even with the NA12878 bam file that is used in the publication examples.

I assume this is part of the pipeline for 1000 genomes analysis so the tool is most likely good and I must really be missing something here.

ADD REPLYlink written 7.1 years ago by Vivek2.3k
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