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How to start CNV analysis via Plink?
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5.7 years ago
mm_taqi • 0
@mm_taqi14130

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

CNV • 2.2k views
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I have tried this, didnt work

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

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Hi, page is not found..

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5.7 years ago
jglessnd • 20
@jglessnd18910

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: http://penncnv.openbioinformatics.org/en/latest/user-guide/input/ If you are using Affymetrix, see here: http://penncnv.openbioinformatics.org/en/latest/user-guide/affy/ 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: http://pngu.mgh.harvard.edu/~purcell/plink/cnv.shtml

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