How to convert SNP genotype data to numerical data?

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7.0 years ago

mysisayk ▴ 20

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?

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ADD COMMENT • link updated 7.0 years ago by bioinfovs ▴ 10 • written 7.0 years ago by mysisayk ▴ 20

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Use plink --bfile file --recodeA

ADD REPLY • link 7.0 years ago by bioinfovs ▴ 10

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

ADD REPLY • link 7.0 years ago by zx8754 11k

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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

ADD REPLY • link 7.0 years ago by mysisayk ▴ 20

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