illumina raw genotype data format

[nans_bn]

Hello,

I was wondering if anyone could help me out with understanding the format or share links where I could infer the genotype data produced from Genome Studio Illumina 2.5 export.

I wish to know the meaning mainly for "Allele1 - Forward" "Allele2 - Forward" "Allele1 - Top" "Allele2 - Top" "Allele1 - Design" "Allele2 - Design" "Allele1 - AB" "Allele2 - AB" .

Your help is appreciated.

Thank you.

[rbagnall]

Resurrecting an old post here, but I need help with a related issue. Illumina have a note describing their system for genotype calling from array data

http://www.illumina.com/documents/pr...ote_topbot.pdf

My problem is that I have genotypes from an illumina cyto12 genotyping array and exome SNP calls from the same samples (human). I would like to assess how well the genotypes match (or not) but I am stuck trying to get the illumina array genotypes to correspond to the human reference sequence strand - as used by GATK.

Any suggestions? - currently I am limited to comparing zygosity between the two methods (homozygous AA, BB; or heterozygous AB), but would really like to compare alleles called by both methods.

Thanks