Question: How to convert SNP genotype data to numerical data?
0
gravatar for mysisayk
2.2 years ago by
mysisayk0
mysisayk0 wrote:

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 • 1.9k views
ADD COMMENTlink modified 2.2 years ago by bioinfovs0 • written 2.2 years ago by mysisayk0

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by zx87547.5k

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 REPLYlink modified 2.2 years ago • written 2.2 years ago by mysisayk0

Use plink --bfile file --recodeA

ADD REPLYlink written 2.2 years ago by bioinfovs0
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