This repository contains the scripts used to compute MutScore, do figures and analysis included in the manuscript and for the two Shiny apps: MutScore and mutScore-batch.
The Shiny apps can be found at: https://iob-genetic.shinyapps.io/mutscore/ https://iob-genetic.shinyapps.io/mutscore-batch/
The scripts used from ANNOVAR and the variants from HGMD database are not present in this repository due to protection of the data by licences.
- BCFTools [Link] (>= v1.9)
- BEDTools [Link] (>= v2.25.0)
- Perl [Link] (>= v5.22.0)
- R [Link] (>= v3.2.0)
- Picard [Link]
The scripts do not require compilation.
-
00_databases-preprocessing.sh
-> Download and processing of databases (ClinVar, ANNOVAR, dbNSFP4.0, CONDEL, ClinPred, OMIM, gnomAD and pext scores).
-
01_clinvar_v0.8-all.sh
-> Annotation of ClinVar, dbNSFP4.0 and gnomAD variants and parsing of the files.
-
02_mutscore-computation-plots.R
-> Processing of the annotated variants: computation of the amino-acid change and positional scores. -> Computation of MutScore model and scores. -> Analysis and figures used in the manuscript.
-
03_cross-validation.R
-> Cross-validation on the training set with figure used in the manuscript.
-
04_MutScore-annotation.sh
-> Annotation of all possible missense with MutScore.
-
05_LiftOver.sh
-> Conversion of scores in hg19 to hg38.
-
06_data-for-mutland.R
-> Processing of the data for MutLand plots.
-
07_Shiny_preprocesssing.R
-> Preprocessing of data for the two Shiny apps.