Illumina top strand genotyping data

posted on 07:27 AM on Wednesday 26 April 2017

Due to the way that Illumina encodes their genotypes ( https://www.illumina.com/documents/products/technotes/technote_topbot.pdf ), 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.