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Old 07-01-2016, 06:37 AM   #1
dan
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Location: Cambridge, England

Join Date: Jul 2008
Posts: 266
Default How to read an Affymetrix Axiom genotype (array data) file?

Hi,

I'm trying to put together genotype data for wheat samples from this resource:
http://www.cerealsdb.uk.net/cerealge...m_flapjack.php

The two types of file I get look like this (array probe set):
Code:
Affymetrix Code,Bristol Affy Code,Bristol SNP Code,Bristol Contig Code,Sequence (including SNP ambiguity code)
AX-94381124,BA00222391,No BS code,GJKKTUG01CGTKM_219,...ACGCA[R]ACNTC...
AX-94381126,BA00232763,No BS code,FZU8VVO01APRT5_148,...TCACT[Y]GNGTG...
AX-94381127,BA00233916,No BS code,contig77177_250,...CCCGA[M]NCGAC...
...
and (Array data):
Code:
A_mutica,A_speltoides,Adhoc,Ae_caudata,Akteur,A...
AX-94381124,1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,...
AX-94381126,1,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2
AX-94381127,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2...
...
The only other information provided about the files is this explanation:
0 = AA, 1 = AB, 2 = BB, -1 = No call

So the question is, what information is required to map from genotype 'score' to actual genotype? Obviously heterozygous calls are clear and distinguished from homozygous calls, but is A. speltoides AA or GG at AX-94381124?

Are these actually Affymetrix Axiom format files, or just something custom?


Thanks for help,
Dan.
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