Cnv List File

Question

[swrdyani]

I have a CNV analysis to be done by plink, I have got the allumina data files as PED, MAP and TXT report files, do I need CNV list file to do the rare CNV analysis, and if I need it how can I create it, thanks in advance for the help

Answer 1

[zx8754]

http://pngu.mgh.harvard.edu/~purcell/plink/cnv.shtml

The CNV list file mydata.cnv has the format
     FID     Family ID
     IID     Individual ID
     CHR     Chromosome
     BP1     Start position (base-pair)
     BP2     End position (base-pair)
     TYPE    Type of variant, e.g. 0,1 or 3,4 copies
     SCORE   Confidence score associated with variant 
     SITES   Number of probes in the variant

[swrdyani]

Thank you very much for your response, this information is available in plink tutorial, I am looking for the steps of creating CNV list file from the data files I got from illumina analysis