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CNV module VS SV module: very tiny overlap

marcpmarcp new yorkMember

Hello,
I'm running GenomeStrip 2.0.1592 both SV and CNV modules on the same sample NA12878.
But I'm getting a very tiny overlap between the "Pass" Calls.

Range SVcalls CNVcalls Overlap
1 0 0 0
300 0 0 0
500 43 0 0
700 112 154 1
1000 393 805 3
5000 107 24 2
10000 36 3 1
50000 15 0 0

I think there is something wrong with the CNV module. In fact one problem might be I'm getting many fragment calls, as pointed out already in this discussion:
http://gatkforums.broadinstitute.org/gatk/discussion/7761/genomestrip-cnv-results-wonky

Can you please help me out with that?

Any help would much appreciated.

Thanks a lot in advance.
Best regards.
Marc

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