Illumina top strand genotyping data

posted on 07:27 AM on Wednesday 26 April 2017

Due to the way that Illumina encodes their genotypes ( ), the following are the possible allele pairs for a top strand file:

  • A/G

  • A/C

  • A/T

  • C/G
    So one can check for a top strand file by checking the genotype frequencies. If only these pairs exists, then it is probably top strand. If C/T and G/T exists, then it is not top strand.