How To Check The Concordance Of Genotypes In Duplicate Samples In Bed And Ped Formats (Produced Via Plink)

Hi does anyone know of a program/software in R or python or even stand alone that checks concodance of genotypes in duplicate samples?

I have 1000 genotyped samples with 50 duplicates. I want to ensure that the genotypes called in each duplicate pair match up, and I want to find the rate of match and mismatch.

Anyone know of a tool that can do that?

genotype qualitycontrol snps duplicates

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updated 12.7 years ago by Istvan Albert

• written 12.7 years ago by snp_cook12 •

what format is your data in?

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written 12.7 years ago by Istvan Albert

these are bed and ped files generated for analysis in PLINK. thanks!

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written 12.7 years ago by snp_cook12 •

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