Manta Structural Variant Caller

Version: NOT RELEASED

Manta is a tool to call structural variants and indels from short paired-end sequencing reads. It combines paired-end and split read evidence during SV discovery and scoring to improve performance, but does not require split reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence of an imprecise variant. It provides genotypes and quality scores for variants in single diploid samples, and will also call somatic variants when a matched tumor sample is specified. Manta can detect all classes of structural variants which can be identified in the absence of copy number analysis and large-scale assembly. See the user guide for a full description of capabilities and limitations.

Build instructions

For Manta users it is strongly recommended to start from one of the release distributions of the source code provided on the Manta releases page. Acquiring the source via a git clone or archive could result in missing version number entries, undesirably stringent build requirements, or an unstable development intermediate between releases. Additional build notes for developers can be found below.

Note that this README is NOT part of an end-user release distribution.

Prerequisites

Manta has been built and tested on linux systems only. It is currently maintained for Centos5,6 and Ubuntu 12.04.

Compilation prerequisites:

• python 2.4+
• gcc 4.1+ OR clang 3.2+
• libz (including headers)

Runtime prerequisites

• python 2.4+

Prerequisite package names (RHEL/Centos)

• g++
• make
• zlib-devel

Build procedure

After acquiring a release distribution of the source code, the build procedure is:

• Unpack the source code
• Create a separate build directory (note an out-of-source build is required.)
• Configure the build
• Compile
• Install

Example:

wget https://github.com/StructuralVariants/manta/releases/download/vA.B.C/manta-A.B.C.tar.bz2
tar -xjf manta-A.B.C.tar.bz2
mkdir build
cd build
../manta-A.B.C/src/configure --prefix=/path/to/install
make
make install

Note that during the configuration step, Manta will build the following compilation dependencies if these are not found:

• cmake 2.8.0+
• boost 1.49.0

To optionally avoid this extra step, ensure that (1) cmake is in your PATH and (2) BOOST_ROOT is defined to point to boost 1.49.0 (the boost version is required to be an exact match). If either of these dependencies are not found, they will be built during the configuration step, To accelerate this process it may be desirable to parallelize the configure step over multiple cores. To do so provide the --jobs argument to the configuration script. For example:

${MANTA_SRC_PATH}/configure --prefix=/path/to/install --jobs=4

Compiling Manta itself can also be parallelized by the standard make procedure, e.g.

make -j4
make install

To see more configure options, run:

${MANTA_SRC_PATH}/configure --help

Data analysis and Interpretation

After completing the installation, see the Manta user guide for instructions on how to use Manta, interpret results, and a high-level overview of the method. The user guide can be found in:

${MANTA_INSTALL_PATH}/doc/html/mantaUserGuide.html

Developer build configuration

When the Manta source is cloned from github, it is configured for development rather than end-user distribution. As such, all builds include -Werror. If cppcheck is found any detected issue is converted to a build error.