Fig. 1

The relationship between phasing and block determination in haplotype association analysis: a Outline of the core steps within a standard SNP-based and a haplotype association analysis, highlighting the additional complexity of the haplotype-based approach. b the effect of block determination given a phased sequence. Here, we show a haplotype from 10 heterozygous SNPs. While all the alleles should all be allocated to the same allele, 2 have been allocated to the maternal v (marked as M in red) and the remaining to the paternal sequence (marked as P in black). As such, the phased sequence has 2 switches (phasing errors) at the loci 5 and 7 and hence has a switch error of 2/10 (20%). If we chose a 3-SNP sliding window with one SNP step, we find that 4/8 (50%) of the blocks contain errors. However, if a 5-SNP window was used, all blocks will contain errors. Using different window sizes affect the error rate within the blocks, yet switch error calculated at the whole sequence scale is constant 20%