Question: Extract genotype at single locus for all individuals in a PLINK binary ped file?
1
gravatar for dam4l
22 months ago by
dam4l170
dam4l170 wrote:

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 • 962 views
ADD COMMENTlink written 22 months ago by dam4l170

Plink is well documented, read about --extract and --make-bed.

ADD REPLYlink modified 22 months ago • written 22 months ago by zx87549.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1067 users visited in the last hour