Pipeline for running the FACETS copy number caller using Snakemake https://snakemake.readthedocs.io/en/stable/
Simple SNAKEMAKE pipeline for running the FACETS copy number https://github.com/mskcc/facets caller on a list of matched tumor/normal bams
Requires the snp-pileup code from https://github.com/mskcc/facets/tree/master/inst/extcode be compiled according to instructions and in the same folder as the facets.snakefile
To do so, save the "snp-pileup.cpp" and "snp-pileup.h" files into the same folder as the facets.snakefile.
Instructions below from the FACETS github:
First, HTSlib must be installed on your system. To do that, download it from http://www.htslib.org/download/ and follow the "Building and installing" instructions on that page. If installed systemwide (in /usr/local/lib) using "make install" ensure that the libraries are available with the command "sudo ldconfig" (only needs to be run once).
This code can be compiled using
g++ -std=c++11 snp-pileup.cpp -lhts -o snp-pileup
when htslib is available systemwide, or
g++ -std=c++11 -I/path/htslib/include snp-pileup.cpp \\
-L/path/htslib/lib -lhts -Wl,-rpath=/path/htslib/lib -o snp-pileup
when it is installed locally and path is the location where it is available. "
a working version of samtools should have the HTSlib installed, if your machine has samtools, you have HTSlib
Please cite original papers.