I have a several families trio of WES data for analysis of possible autosomal dominant condition and X linked variants. Variant calling of SNPs/indels does not detect any mutations in the relevant genes. There is high chance that there is Copy number variant causing the condition. However, I am not sure which CNV caller should I use.
I have reading literature and find several calling set. I am aware that its difficult task to do especially with false positive rate. Also, the golden stander methods is to use aCGH method. However, to reduce the cost I would like to call CNV from BAM files that already generated.
1st approach: GATK4 gCNV uses very good approach, but not very sure if their COHORT mode would be applicable on data that I have. I am not sure what they meant by COHORT mode. Is COHORT for unrelated individuals. or Its OK to use a family pedigree to see the differences between a child with their parents.
2nd approach; Exome Depth, CNVkit, XHMM and others are very good tools. But I have seen researchers used multiple calling methods and then used statical approach to narrow down the error rate.
I am open for both ways but I would be happy if anyone have similar experience can give more details, please.
Thank you Faisal