Hi Sam, Section 2 of the vignette "GWAS Data Cleaning" contains an example of how to import raw illumina data of exactly this type into GWASTools. The example data is contained in the package "GWASdata." If you have any further questions after reading the vignette, please cc the bioconductor mailing list (bioconductor at r-project.org). Section 7 may also be of use to you, as it deals with chromosome anomaly detection. best wishes, Stephanie On 4/23/13 7:54 PM, Sam Rose wrote: > Hi Stephanie, > > My name is Sam Rose and I am contacting you the GWASTools package in > Bioconductor of which it says you are the maintainer. > > I am trying to use the package to call mosaic CNVs in my samples and > can't seem to get it to work. > > I'm wondering if you have an example of the raw illumina data to put in > there, and maybe examples of some of the things required in the > 'ncdfAddData' command (i.e. sample column, col.nums). I have created the > shell ncdf file, but beyond that the headers and data formats seem to be > giving me trouble so I just though I would ask. > > Our Illumina raw data files look like this: > SNP_NameChromosomePositionGC_ScoreAllele1_-_TopAllele2_- _TopAllele1_-_ABAllele2_-_ABXYRaw_XRaw_YR_IlluminaTheta_IlluminabAllel e_FreqLog_R_Ratio_IlluminaR_TrigTheta_TrigLog_R_Ratio_Trig > rs44772121720170.38423407AAAA0.393692269026780450.025018186414745233 8333240.41871045544152570.040401312884379780.006063504097364059-0.6120 798296992830.394486390567453940.06346223387647508-0.6182450719587295 > > Thanks for your help, > > Sam > > -- > ----- > *Sam Rose, Stanley Center Research Associate II > Stanley Center for Psychiatric Research, The Broad Institute > 7 Cambridge Center, Cambridge, MA 02142* > 617.714.7853, srose at broadinstitute.org <mailto:srose at="" broadinstitute.org=""> >