CNV tools for WGS data
1 answer
CNVnator and cn.MOPS are good starting points. Also look at Pindel to find smaller duplications and deletions.
If you're able to run multiple callers, consider using MetaSV to consolidate the results from all callers. This will improve your accuracy at all scales and simplify the rest of your analysis by combining the calls into a single VCF.
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