Figure 1.

GIPS workflow. The impacts of diverse experimental and analysis choices on the chance of an analysis procedure to successfully identify the phenotype-associated gene can generally be summarized into their impacts on two sample-wise analysis effectiveness indicators: the sensitivity and specificity for each sample with which the analysis procedure is able to detect the phenotype-causing variants. Sensitivity and specificity are affected by the genomic region being sequenced, the quality and depth distribution of sequencing reads, the choice of software and parameters to align sequencing reads, the choice of software and parameters to call variants, and the choice of strategies to filter variants that are unlikely to associate with the phenotype.