Changing the ratio affects the probability with which an observed relative variant frequency is interpreted by the model as a phenotype linked region (see also below).
Changing the αP/βP ratio affects the emission probability or the probability with which an observed relative variant frequency is interpreted by the model as a phenotype linked region.
A first set of methods model LD in a mere data driven way: relative variant frequencies are fitted robustly fit using a sliding window based strategy followed by different smoothing functions [ 3, 7, 9, 11, 12].
The ratio between αP and βP thus defines the degree to which the relative variant frequency at a marker site needs to differ from the one obtained through random inheritance for it to be called linked to the phenotype (stringency of the method).
The Common Target File allowed us to evaluate relative variant sensitivity without regard to platform-specific target design.
Variants were identified using the variant identification module included into V.I.P. with filter settings: homopolymers < 7, Quality score ≥ 30, relative variant frequency ≥ 0.35 and total coverage ≥ 20.
Sequence data with genes, exons, coding regions and strand-dependent codons are marked at appropriate zoom levels, and tracks summarizing GC content, relative variant density and results from data analysis are presented.
Experimental verification of QTL2 on chromosome X was based on determining for a selected set of marker sites in this region, the number of times individual segregants selected for high ethanol tolerance displayed the variant originating from the superior parent (relative variant frequency in individual segregants) [ 3].
To identify the relative variant frequencies in the pools of segregants at marker sites, we implemented a custom script to count at each marker site the number of read alignments that support the variant originating from the superior parent (VR1-5B) and the total number of alignments.
Relative variant frequencies in individual segregants were used to calculate the posterior probability of each marker site to be linked to the phenotype of interest using an exact binomial test with a confidence level of 95% and correction for multiple testing by a false discovery rate (FDR) control according to Benjamini and Yekutieli [ 20].
