Recommendations on PLINK for CNV analysis

Question

[stevenlang123]

I have generated CNV calls for ~20 multiplex families (more than one affected) for a single dichotomous trait. Does anyone have any recommendations on how to use PLINK (or another tool) to help identity causative CNVs?

-Best

Steven

Answer 1

[jglessnd]

Try ParseCNV. You can run ParseCNV --tdt for family based analysis. ParseCNV --includePed will make a standard Plink Bed/Bim/Fam for family based analysis functions in Plink.

[stevenlang123]

Thank you, do you know if controls are necessary in an a family based analysis? Additionally, ParseCNV asks for ChrSNP map my calls were made using sequence data, not array data...

[jglessnd]

If there are no control subjects as in a family based or quatitative trait association study, use the file NullControl_ForQuantitativeTrait.rawcnv for the Controls.rawcnv input.

If you are using sequencing data or are uncertain about the full set of probes, a blank or incomplete file can be used as the map input and the map will be dynamically determined by the start and end positions (breakpoints) of the CNVs observed in the .rawcnv files.