Question: Questions running Delly to detect copy number variation
1
gravatar for mavershang
4.3 years ago by
mavershang50
United States
mavershang50 wrote:

Hi there. I am running delly to detect CNV.

There are 6 BAM I need to run. Is there any difference if I run it like

delly -t DUP -o sample1.out -g ref.fa sample1.bam
delly -t DUP -o sample2.out -g ref.fa sample2.bam
...
delly -t DUP -o sample6.out -g ref.fa sample6.bam

# and then merge the output vcfs

 

Versus

 

delly -t DUP -o allSamples.out -g ref.fa sample1.bam sample2.bam sample3.bam sample4.bam sample5.bam sample6.bam

 

Thanks

cnv delly • 1.6k views
ADD COMMENTlink modified 4.3 years ago by Zev.Kronenberg11k • written 4.3 years ago by mavershang50
2
gravatar for Zev.Kronenberg
4.3 years ago by
United States
Zev.Kronenberg11k wrote:

Second sentence of the methods section in the Delly paper:

"All input libraries are analyzed jointly to achieve optimal sensitivity."

specificity > sensitivity  : call separately 

sensitivity > specificity  : joint call

 

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Zev.Kronenberg11k
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