When it is recommended to use "detect_cnv.pl -test" and "detect_cnv.pl -validate"?
I ran "detect_cnv.pl -test" in 2000 cattle samples on 100K and I got all the frequencies for all the CNV regions discovered. After that, I ran "detect_cnv.pl -validate" on the same samples, using the prior frequencies for all the CNV regions discovered in the "test" step. However, the "validate" algorithm has called much more deletions and duplications, for the fixed regions, that haven't been detected by the HMM algorithm, i.e., for sample1-region1 there was no CNV using "detect_cnv.pl -test" but a duplication using "validate". Could you help me understand when using "test" and "validate" and why a difference in the results?
Hello,
When it is recommended to use "detect_cnv.pl -test" and "detect_cnv.pl -validate"?
I ran "detect_cnv.pl -test" in 2000 cattle samples on 100K and I got all the frequencies for all the CNV regions discovered. After that, I ran "detect_cnv.pl -validate" on the same samples, using the prior frequencies for all the CNV regions discovered in the "test" step. However, the "validate" algorithm has called much more deletions and duplications, for the fixed regions, that haven't been detected by the HMM algorithm, i.e., for sample1-region1 there was no CNV using "detect_cnv.pl -test" but a duplication using "validate". Could you help me understand when using "test" and "validate" and why a difference in the results?
Thank you