Questions running Delly to detect copy number variation

Question

[mavershang]

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

Answer 1

[Zev.Kronenberg]

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