1. 

   ldowns
   

   Member
   Joined: Jul '10
   Posts: 1

   
   Posted Jul 20, 2010 #

   I have a marker set of over 180 000 SNPs, but am struggling to get hold of the standard alleles for the set.

   I am under the impression (from the user manual) that the standard alleles are optional, and therefore not required, but when I try to import the genotyping data it all gets rejected with the message "Invalid SNP (no allele match for ACTG)".
   I am certain it has to do with the standard alleles, because I have worked them out from the genotyping data for a couple of markers, and when the markers have standard alleles defined, the genotype imports work perfectly.

   Please can someone help me with this?

   Thank you
2. 

   Conrad Brammer
   

   Progeny Staff
   Joined: Dec '08
   Posts: 123

   
   Posted Aug 11, 2010 #

   I am assuming that when you are importing your genotypes that you are importing ACGT format, but please correct me if I am wrong.

   Importing the standard alleles is optional for the marker set, but it is necessary for handling ACGT genotypes. If you do not import the standard alleles for the set, then the genotype data you import must be in AB format. If you intend to import ACGT genotypes, you need to import the standard alleles to translate that data.

   Thank you for your post.

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