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

Note

Most users will want to install LoFreq via BioConda! The source code hosted here on Github is mainly for developers!

LoFreq was published 10 years ago, is considered very stable and has almost 1000 citations at the time of writing this. I (Andreas) have long left academia and tried to maintain the code as best as I could until now, but find that I have no more time to do this. For bugs, suggestions, ideas, collaborations please contact Niranjan Nagarajan.

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)