Questions running Delly to detect copy number variation
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Entering edit mode
7.7 years ago
mavershang ▴ 60

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 • 2.6k views
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3
Entering edit mode
7.7 years ago

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

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