*2.3.2. Homopolymer errors*

Homopolymer errors in reads of Roche 454 and Ion Torrent sequencers are common, but actually hardly effect the genotyping results. It is because aligner algorithms are dealing differently with flow-space and letter-space reads (Illumina reads are belonging to the latter category) and indels are tolerated by introducing a different error model into the aligner. Nevertheless, alleles differing in the length of the homopolymer can be displayed as ambigu‐ ities, such as HLA-A\*03:21N where there is an insertion in the originally 7 bases-long C homopolymer in exon 4 of the allele compared to HLA-A\*03:01:01:01. Similar to this null allele, pseudogenes, such as HLA-H, the pseudogene related to HLA-A can occur in typing results, particularly in typing from whole-genome data as these HLA-H alleles differ from the corresponding HLA-A alleles in the length of homopolymers.

Homopolymer errors occur for Illumina reads as well, though mainly arising not from the signal detection technology itself but due to polymerase slip on a homopolymer stretch [33]. A variation on polymerase slip is when it is not the length of the homopolymer that is changed, but a base surrounded by two homopolymers such as CCCCACCCC changing to CCCCCCCCC.
