pdivas 1.0.0

PDIVAS: Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing

PDIVAS : Pathogenicity Predictor for Deep-Intronic Variants causing Aberrant Splicing

Sumary

• PDIVAS is a pathogenicity predictor for deep-intronic variants causing aberrant splicing.
• The deep-intronic variants can cause pathogenic pseudoexons or extending exons which disturb the normal gene expression and can be the causal of patiens with Mendelian diseases.
• PDIVAS efficiently prioritizes the causal candidates from a vast number of deep-intronic variants detected by whole-genome sequencing.
• The scope of PDIVAS prediction is variants in protein-coding genes on autosomes and X chromosome.
• This command-line interface is compatible with variant files in VCF format.

PDIVAS is modeled on random forest algorism to classify pathogenic and benign variants with referring to features from

1. Splicing predictors of SpliceAI (Jaganathan et al., Cell 2019) and MaxEntScan (Yao and Berge, j. Comput. Biol. 2004)
   (*)The output module of SpliceAI was customed for PDIVAS features (see the Option2, for the details).

2. Human splicing constraint score of ConSplice (Cormier et al., BMC Bioinfomatics 2022).

Reference & contact

bioarxiv?
[e-mail] (Ryo Kurosawa at Kyoto University)

Details

Please view the detailed usage and methods at https://github.com/shiro-kur/PDIVAS and medRxiv.