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PennCNV joint-calling algorithm The joint CNV calling algorithm in the PennCNV package is designed for calling CNVs from parents-offspring trios and has improved performance over the trio calling algorithm described in previous Trio Calling tutorial section. Please see the Wang et al paper in NAR for details on the joint calling algorithm. (The current joint-calling algorithm has been re-written and been directly incorporated into the main detect_cnv.pl program.) Unlike the trio calling algorithm, which use posterior validation on individual-based CNV calls, the joint-calling algorithm generates CNV calls in one single step for three individuals in a family. The joint-calling algorithm has better performance than the current family-based CNV calls, especially in resolving the correct CNV boundaries and for reducing false negative rates on very small (<10 SNPs) CNV calls. However, it is extremely slow and may take several hours for a single trio genotyped at 550K markers. To use this new algorithm, the user can specify --joint argument, rather than --trio argument in the command line. For example:
[kaiwang@cc penncnv]$ detect_cnv.pl -joint -hmm lib/hh550.hmm -pfb lib/hh550.hg18.pfb sample1.txt sample2.txt sample3.txt -out sampleall.jointcnv As we can see from the command line above, unlike the -trio argument, the joint-calling algorithm does not require a CNV file generated by individual-based calling algorithm as input files. The joint-calling algorithm only supports trios. For complex nuclear families, it is better to be processed with the -trio and -quartet operations described in Trio Calling section in the tutorial. |