The method copes with inaccurate estimates of variant noise patterns in the image, showing its robustness in realistic cases.
Most of the estimates of variant frequency for these rare conditions are based on the prevalence of a particular disorder in a population, rather than the prevalence of pathogenic allelic variants for that condition.
Thus there are two major advantages to iterative remapping: locally, enhanced detection of variants at both high and low frequencies in areas with dense mutation rates and globally, significantly better estimates of variant frequencies.
Building on a prior study in which we deeply sequenced 31 somatic genomes of tumors, neoplasias, and controls in six patients [ 16], we here obtain much more accurate estimates of variant allele frequencies (VAFs) of phylogenetically informative single nucleotide variants (SNVs) in a much greater number of samples, with emphasis on pre-invasive neoplasias.
Thus, besides using 'class' number as the estimate of splice variant number, we have also used a weighted method such that a class was counted as 0.5 splice variant if it followed the above two situations.
Finally, the SnpEff annotations also provide an estimate of the variant impact on the protein function [ 25].
This yielded a conservative estimate of RIG variant calls whereby 95% sensitivity and 99% positive predictive value are achieved in one tranche with the RIG workflow (the 99.0% tranche in this case).
The winner's curse is the phenomenon that the association estimate of the variant with the strongest association from a GWA study tends to be overestimated [Göring et al., 2001].
In case of dichotomized outcomes the effect size estimates of the variant is given as the odds ratio (OR) in those carrying the variant allele compared to non-carriers.
VariantMetaCaller uses Support Vector Machines to combine multiple information sources generated by variant calling pipelines and estimates probabilities of variants.
