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Bryce van de Geijn edited CHT intro.tex
almost 10 years ago
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\subsection{The combined haplotype test}
The combined haplotype test (CHT) tests whether the genotype of a ``test SNP'', $m$, is associated with read depth and allelic imbalance within a nearby ``target region'', $j$, on the same chromosome. A single target region may be discontiguous and span multiple genomic loci. For example, the exons of a gene can be used as a single target region, which is useful when searching for expression QTLs using RNA-seq reads. The test SNP is not required to be within the target region, but is assumed to be nearby and cis-acting. This allows us to combine information from across phased heterozygous SNPs and assign reads to one haplotype or the other.
