A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data

. Author manuscript; available in PMC: 2013 Jul 31.

Published in final edited form as: Stat Appl Genet Mol Biol. 2012 Jan 6;11(2):10.2202/1544-6115.1713 /j/sagmb.2012.11.issue-2/1544-6115.1713/1544-6115.1713.xml. doi: 10.2202/1544-6115.1713

S₄₀₀	the probability the parental zygotic alleles have the spectrum 4-0-0
S₃₁₀	the probability the parental zygotic alleles have the spectrum 3-1-0
S₂₂₀	the probability the parental zygotic alleles have the spectrum 2-2-0
S₂₁₁	the probability the parental zygotic alleles have the spectrum 2-1-1
*S_M*	the number of nucleotide mismatches between m^* and o_a
*S_F*	the number of nucleotide mismatches between f^* and o_b
*S_Som*	the number of nucleotide mismatches between all x and x′
*S_Hom*	the number of nucleotide matches between a somatic homozygous genotype and its sequencing reads
*S_Het*	the number of nucleotide matches between a somatic heterozygous genotype and its sequencing reads
*S_E*	the number of nucleotide mismatches between a somatic genotype and its sequencing reads.