Shannon pipeline

[…] reasons for our selection of strelka). protein coding mutations were annotated by annovar and splicing mutations with the shannon human splicing pipeline (, see for a list of all mutations). the shannon pipeline predicted significantly more splicing mutations than reported by tcga, because the information-theoretic method employed enables analyses of variants beyond exon boundaries […]

[…] information weight matrices (based on the method described by schneider et al. 1984; n = 147) (see additional file : methods) []. all utr variants were assessed using a modified version of the shannon pipeline [] containing the rbpdb and cisbp-rna models. results were filtered to include a) variants with |δri| ≥ 4.0 bits, b) variants creating or strengthening sites (ri,final ≥ rsequence […]

[…] was used with default parameters to predict which variants are likely to affect amino acid sequence and splicing at the natural splice sites. the shannon human splicing pipeline version 2.0 (shannon pipeline) was used to complete a more in-depth analysis of splicing mutations, which predicts variants that will alter the binding affinity of the natural site or cause cryptic splicing (i.e. […]