LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data

Note

Most users will want to use either the binary or the source-code package. Both are distributed via LoFreq's Sourceforge site. The source hosted here on github is mainly for developers!

Building the Source

Current Build Status

Prerequisites

You will need:

• a C compiler (e.g. gcc or clang)
• a Python 3 interpreter
• zlib developer filesi (zlib1g-dev on Ubuntu)
• a compiled version of HTSlib 1.4 or later

Compilation

• Clone the repo (or download the current master as zip package and unpack)
• Run ./bootstrap to set up the required automake files
  • If you get an error like required file './ltmain.sh' not found, run libtoolize (or glibtoolize) first and then bootstrap again
  • Subsequent pulls won't require rerunning ./bootstrap. This is only necesary when changing configure.ac or any of the Makefile.am
• Run ./configure with the absolute path to HTSlib (e.g. ./configure --with-htslib=/home/user/miniconda [--prefix=inst-path])
• Run make
  • At this point you can already start using lofreq: ./bin/lofreq
• Run make install to properly install the package
  • Default is /usr/local/. If --prefix was given to configure, the corresponding argument is used
  • Depending on the used prefix you might need to adjust your PATH (and PYTHONPATH).

Documentation

• Simply calling lofreq on the command line will display a list of subcommands
• lofreq cmd will then display help for cmd
• See LoFreq's website for full documentation

License

LoFreq is licensed under the MIT License (see LICENSE).

Licenses for third party software that is part of the source:

• cdflib90 (see src/cdflib90.README)
• uthash (see src/uthash/LICENSE)