How to start CNV analysis via Plink?

Question

[mm_taqi]

I have Bed, BIM and Fam files. I want to analyse CNVs via PLINK. I need assistance, how I may convert these files to the ones required for CNVs analysis via PLINK. Thanks

[Giovanni M Dall'Olio]

Check the plink tutorial: http://pngu.mgh.harvard.edu/~purcell/plink/gvar.shtml

[mm_taqi]

I have tried this, didnt work

[smilefreak]

Do you happen to have the errors you got when you tried this?

[lovegenetics]

Hi, page is not found..

Answer 1

[jglessnd]

You cannot convert Plink Bed/Bim/Fam into Plink CNV. You need to use the Illumina Genome Studio Project with the Idats from your samples loaded and export BafLrr files. Use column chooser to show B allele Freq and Log R Ratio along with SNP Name, Chr, and Position. Use the PennCNV packaged script kcolumn.pl to convert the all samples text file into single sample text files. See detailed instructions here. If you are using Affymetrix, see here. Once you have generated a PennCNV .rawcnv file (using the --conf option), you can convert into a Plink CNV file using a simple bash command:

sed 's/:/\t/' Cases_wConf.rawcnv | \
  sed 's/-/\t/' | sed 's/chr//' | sed 's/state.\,cn\=//'| \
  sed 's/conf=//' | sed 's/numsnp=//' | \
  awk '{print "0 "$7" "$1" "$2" "$3" "$6" "$10" "$4}'

or use ParseCNV which uses PennCNV .rawcnv as input directly. See Plink CNV format specification here