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Welcome to the expressed-variant-reporting wiki!
SnpReportR is a program to generate clinical and research reports of patient-derived RNA-seq data, using annotated .vcf files.
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]
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]
The VCF_report_rendering.R R script must be edited to include the location of the configuration file.
Invoke the R script VCF_report_rendering.R to run SnpReportR.