All annotated CNV calls are available in "CNV_Segments_Annotated.txt".
CNV Calling done using the CamCNV pipeline here: https://github.com/jgd29/CamCNV Settings used are specified in the supplementary methods.
The by probe association tests were run using the logit program. http://ccge.medschl.cam.ac.uk/software/mlogit/ There are there no additional options, just: -i arg input file -p arg phenotype file -o arg output file
RAML is available here: http://ccge.medschl.cam.ac.uk/software/raml/ The settings used for RAML were: raml -r 0.6 -m 0.01 -n 10000 -r arg r2 at which to merge correlated variants (default 0.9) -m arg maximum maf for rare alleles -n arg number of permutations (default 10000)
All other main analysis scripts and files for easy running of these scripts are available in "analysis_scripts" and "analysis_files".
The simulated background files for the enrichment analysis are too large for normal Github storage. They can be easily generated with the available uploaded files using "Script_Initial_File_Conversion.sh" if needed.