CovApp v1.1

CovApp is an R shiny app that shows gene coverage boxplots for in-house WES data. See ./CovApp/App.R for application code.

Data Sources

CovApp app renders plots using three source files:

• covtidy.txt lists the percentage coverage above 20X for each gene in each sample.
• covtidy_genes.txt lists unique genes in covtidy.txt.
• covtidy_median.txt lists the median percentage coverage above 20X for each gene across all samples.

All three source files are generated by create_covtidy.py, a script that requires *.chanjo_txt files output by the WES pipeline.

Deployment

CovApp is hosted at shinyapps.io.

Contact

Viapath Genome Informatics.