Third, we post-process the phase calls to correct sporadic errors. Within each window of three consecutive blocks, we use LSH to determine the frequencies of ≈1cM haplotypes that match the Viterbi-inferred maternal and paternal haplotypes up to at most two errors. In rare cases, the haplotype frequencies give strong evidence to flip the phase of one or two SNPs, in which case we override the Viterbi phase call. Finally, we also check the Viterbi-inferred maternal and paternal haplotypes for consistency with the longest previously-identified IBD segments; in rare cases when the Viterbi phasing requires a phase switch >1.5cM from either end of a probable IBD segment, we override the switch.
