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How to convert SNP genotype data to numerical data?

Description: I have a SNP genotype data (i.e. AA, AC, CA, AG, GA, AT, TA, CC, CG, GC, CT, TC, GG, GT, TG and TT) and BB type) of durum wheat (allotetraploid) obtained from genotyping through 35k axiom array and analysed by Axiom analysis suit v2. Can any one help with how to convert it to numerical data for use in STRUCTURE software?

snp
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updated by bioinfovs • bioinfovs • written by mysisayk • mysisayk

Please provide link to the software webpage/manual. Convert using what tool? How big is the data? What have you tried?

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written by zx8754 zx8754

Hello, zx8754

for structure software: the input data format uses ; A=1, C=2, G=3, T=4 and NoCall(missing value) = -9; so using the numbers will give us AA=11, CC=22, GG=33, TT=44; and any heterozygous will have the combination e.g. AT=14, CG=23 etc.

I don't have strong background with softwares and programing language. So, I tried in Excel to find and replace each but, takes too long and computer gets stuck.

I do hop you will help me to sort out this and many thanks in advance

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written by mysisayk • mysisayk

Use plink --bfile file --recodeA

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written by bioinfovs • bioinfovs

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