Coding biallelic SNP data

[Saad Arif]

Hello

I'm using STRUCTURE for the first time and had a question about coding my SNP data. I have biallelic SNP at each marker for all individuals. I understand the alphabetic SNP data need to be coded numerically (A=1, T=2, C=3, G=4). However, do i need to input each individual in two rows with one allele on the first line and the second on second line? I do not have any phase information. Any input would be appreciated. Thanks in advance.

best,
Saad

[Saad Arif]

Also, individuals are diploid and thus i have two nucleotide information at each marker

[Vikram Chhatre]

Hello Saad,

You can put both alleles on the same line (ONEROWPERIND=1) or on two consecutive lines (ONEROWPERIND=0).  In case of latter, the individual ID should be identical in both lines.

V

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[Saad Arif]

Dear Vikram

Thanks for your response. In the case alleles on the same line per individual, if my marker genotype is AA do i code this as 11 and if it is AT then 12?

Thanks in advance.

Saad

On Tuesday, October 22, 2013 4:39:15 PM UTC+2, Vikram Chhatre wrote:

Hello Saad,

You can put both alleles on the same line (ONEROWPERIND=1) or on two consecutive lines (ONEROWPERIND=0).  In case of latter, the individual ID should be identical in both lines.

V

On Tue, Oct 22, 2013 at 9:37 AM, Saad Arif <arif...@gmail.com> wrote:

Hello

I'm using STRUCTURE for the first time and had a question about coding my SNP data. I have biallelic SNP at each marker for all individuals. I understand the alphabetic SNP data need to be coded numerically (A=1, T=2, C=3, G=4). However, do i need to input each individual in two rows with one allele on the first line and the second on second line? I do not have any phase information. Any input would be appreciated. Thanks in advance.

best,
Saad

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[Vikram Chhatre]

Treat each allele as a distinct entry i.e. write 1 2 instead of 12.  A space or tab is fine, but be consistent.

V

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