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SnpReportR

SnpReportR is a program to generate clinical and research reports of patient-derived RNA-seq data, using annotated .vcf files.

Input File Format

Annotated .vcf

SnpReportR requires an annotated .vcf file containing fields X, Y, and Z, as generated by upstream Collaborative Bioinformatics Pipeline programs X, Y, and Z. See the example annotated .vcf file, below.
[annotated .vcf example .jpeg here]

Currently supported VCF files are from version 2.5.0 of the CTAT Mutations Pipeline. There is a companion CTAT Mutations WDL workflow developed for the DNAnexus cloud platform for easily producing the necessary VCF files from RNA-seq.

Configuration file

Before running SnpReportR, edit the configuration file, config.txt, to direct SnpReportR to the directory containing the SnpReportR program files, the annotated .vcf file, and the output directory. See the example configuration file, below.
[configuration file example .jpeg here]

Step 1.

• configure gmailR package according to quickstart instructions

VCF_report_rendering.R

The VCF_report_rendering.R R script must be edited to include the location of the configuration file.(To Do)

Step 2.

• open VCF_report_rendering.R to edit the following lines below.

#temporary instructions. Will become config file or .Renviron(possibly?) file soon. 

#Edit this if vcf file suffix is different. Keep all data files in Data/. 
#Could use symlinks in Data/ directory if you need to host data on a separate drive. 
files <- dir("Data", pattern="wAnnot.vcf.gz", full.names = TRUE, recursive = T)

#Email Config
sender         <- '[email protected]'
recipients     <- c('[email protected]','[email protected]','[email protected]') #should work for other email hosts need to test

#Rmarkdown Config
Sys.setenv(RSTUDIO_PANDOC="/path/to/pandoc")

Running SnpReportR

Invoke the R script VCF_report_rendering.R to run SnpReportR once you have authenticated the gmail account to use and defined the location of the VCF files. Simply run the following command on the terminal (Mac OSX 10.14.6 tested, likely works on linux OS distributions).

Step 3.

• run the VCF_report_rendering.R script on the command line.

> ./VCF_report_rendering.R

You can expect to render the Rmarkdown analysis HTML report, and have recipients receive the email with the HTML report as an attachment. Estimated time per VCF file is approximately 2 min. The VCF_report_rendering.R script will be updated to have parallelization of rending and sending the emails using foreach R package in the next version (To Do).