sarek.pathfindr

Scoring and ranking somatic and germline variations for cancer research

Original code is at https:/NBISweden/pathfindr developed by Markus Mayrhofer. Still in progress, but it can have some use. It is intended to run on data generated by Sarek, and the goal is to get filtered, ranked somatic and germline variants, optionally in a HTML page, or in an annotated VCF. This page can help in formulating a report, or visualize the most important somatic or germline variants.

To run the code you have to

• run Sarek for a normal/tumor sample, get variant calls for ASCAT, Control-FREEC, HaplotypeCaller (calls for both the normal and the tumor sample), Mutect2 (GATK 3.8 for the moment), Strelka and Manta in somatic mode.
• clone this repo
• create a conda environment using the provided environment.yml file
• edit pathfindr.config.yaml
• run
  • either Rscript runPathfindr.R to have CSV results only
  • or runPF_html.sh to get a HTML file
• after an hour have a look at the results

In RStudio console (or R prompt) after checking out from github and changing to the directory you can have

library(devtools)
install("../sarek.pathfindr")
library(sarek.pathfindr)
...

To get a HTML output, run rmarkdown::render("runPF.Rmd") in the console (or - after installing the proper R5 environment i.e. via conda), do

Rscript <(echo "rmarkdown::render('runPF.Rmd',knit_root_dir='.',output_file='bugger.html')")

Csirz: szilveszter.juhos at scilifelab.se