Extract genotype at single locus for all individuals in a PLINK binary ped file?
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2.4 years ago
dam4l ▴ 180

I have genotype data (Illumina Global Screening Array) from ~700 individuals.

I am also genotyping 1 SNP in using the TaqMan assay, and I need to check the concordance between the chip genotypes and the TaqMan genotypes for all individuals in my sample.

To do this, I need to extract the genotype for all individuals at 1 specific SNP that is genotyped on this array. The data are currently stored in a PLINK bed file. All suggestions are welcome.

SNP plink • 1.2k views
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Plink is well documented, read about --extract and --make-bed.

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