A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium
Allelic specific expression (ASE) increases our understanding of the genetic control of gene expression and its links to phenotypic variation. ASE testing is implemented through binomial or beta-binomial tests of sequence read counts of alternative alleles at a cSNP of interest in heterozygous individuals. This requires prior ascertainment of the cSNP genotypes for all individuals. To meet the needs, we propose hidden Markov methods to call SNPs from next generation RNA sequence data when ASE possibly exists.
allelic specific expression hidden markov model rna-seq data