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Improved Bayesian inversion somatic caller
This project forked from ding-lab/bassovac
Improved Bayesian inversion somatic caller
============================================================================== Compiling Bassovac ============================================================================== ------------------------------------------------------------------------------ 1) Dependencies ------------------------------------------------------------------------------ The build process requires the following tools: CMake 2.8 (http://www.cmake.org) boost 1.40+ (http://www.boost.org) If you are running a recent, debian based distro this may work for you: sudo apt-get install libboost-all-dev cmake ------------------------------------------------------------------------------ 2) Setup build environment ------------------------------------------------------------------------------ First, make sure your checkout is complete by initializing the build-common submodule: git submodule update --init build-common Next, create an out-of-source build directory, change into it, and run cmake with the path to the top of the bassovac checkout. For example, to build in a subdirectory of the checkout called 'build', one runs: mkdir build cd build cmake .. Or to build in /tmp: mkdir /tmp/build-bassovac cd /tmp/build-bassovac cmake ~/path/to/bassovac/checkout ------------------------------------------------------------------------------ 3) Build and test ------------------------------------------------------------------------------ To build, simply run make in the build directory. Once make is finished, you can run the unit test suite by executing 'ctest' from the build directory. All binaries can be found in the bin/ subdirectory where you built. ============================================================================== Output Format ============================================================================== The tab separated output fields are: 1) sequence name (chromosome) 2) start position 3) end position 4) reference base 5) total normal reads at this position 6) # normal reads supporting reference 7) harmonic mean of normal base qualities 8) total tumor reads at this position 9) # tumor reads supporting reference 10) harmonic mean of tumor base qualities 11) probability of homozygous variant 12) probability of heterozygous variant 13) probability of somatic variant 14) probability of loss of heterozygosity event 15) probability of 'non-interesting' event
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