I am interested in CNV detection in Whole Exome sequencing data and I just want to make sure that i'm doing it in proper way.
I have selected a bunch of samples, obtained using one target enrichment set, to create reference file.
Then I used cnvkit.py batch on samples of interest bam files (made with the same target enrichment set).
As stated in manual, for germline analysis I should use cnvkit.py segmetrics with --ci option, following by cnvkit.py call --filter ci sample.segmetrics.cns to get rid of possible FP CNVs.
After that I used cnvkit.py export vcf/bed on resulting sample.segmetrics.call.cns file to get list of confident SV calls for further analysis.
Is it a proper way to search for CNVs in WES data or are there any steps to modify/change?
Is there any field in the CNVkit vcf-file (probes, fold_change_log etc.) by which it is possible to evaluate, how reliable is one particular SV call?
I am interested in CNV detection in Whole Exome sequencing data and I just want to make sure that i'm doing it in proper way.
cnvkit.py batchon samples of interest bam files (made with the same target enrichment set).cnvkit.py segmetricswith--cioption, following bycnvkit.py call --filter ci sample.segmetrics.cnsto get rid of possible FP CNVs.cnvkit.py export vcf/bedon resultingsample.segmetrics.call.cnsfile to get list of confident SV calls for further analysis.Is it a proper way to search for CNVs in WES data or are there any steps to modify/change? Is there any field in the CNVkit vcf-file (probes, fold_change_log etc.) by which it is possible to evaluate, how reliable is one particular SV call?