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Added support for LUMPY, Manta and CNVkit-the input files must be provided as VCFs. Thanks to Brad Chapman ( @chapmanb ) for this enhancement. With this feature, the MetaSV integration in bcbio (thanks to @chapmanb again for this) should work since LUMPY, Manta and CNVkit are already supported in bcbio. Please note that the integration of these tools is still experimental as we work to improve the accuracy of MetaSV for this set of SV-callers.
More documentation has been added on the MetaSV webpage with examples on running MetaSV for different use-cases.