Recode Genotypes

CramerRaoEagle1 — Mon, 21 Aug 2023 19:21:30 GMT

JMP Genomics had a workflow to recode genotypes (matrix - samples in rows, markers in columns), from nucleotide (A,T,C,G) to numeric (major allele = 0, minor allele = 1, hets =2). Now the genomic analysis is offered in JMP pro, I'm not seeing an easy way to do this. I see that you can check recoding, but not to create the original recoded file. Is there a script or add-in that might be available for this? THANK YOU

I am using JMP PRO 17.0.0

Re: Recode Genotypes

Chris_Kirchberg — Wed, 23 Aug 2023 17:56:13 GMT

Hi @CramerRaoEagle1 ,

If we assume diploid and use IUPAC Nucleotides, then the attached script should convert A, C, G, and T's into numeric genotypes (0 major homozygous, 1 heterozygous, and 2 minor homozygous). This also assumes that each SNP has a single IUPAC nucleotide letter in its column.

You would still need to user the Marker Statistics platform to verify the proper numeric coding based on frequency for each column and likely need to recode some of the SNPs. I have added that step to the script as well.

Let us know if this script will work for you

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Recode Genotypes

Re: Recode Genotypes