LRcaller

Program to estimate genotype structural variants from long read data.

Please see the CHANGELOG before updating from v0.2 to a newer version.

Build instructions

Requirements:

• CMake >= 3.4
• SeqAn2 (currently the -develop branch is required!)
• OpenMP
• C++20 capable compiler (tested with GCC≥10 and Clang≥10)

Download or clone this repository with submodules:

mkdir -p ~/devel
cd ~/devel/
git clone --recurse-submodules https://github.com/DecodeGenetics/LRcaller

And then build it:

mkdir -p ~/devel/lrcaller-build/release
cd ~/devel/lrcaller-build/release
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-march=native" ../../LRcaller
make
make test # optional

The -DCMAKE_CXX_FLAGS="-march=native" is not required but highly recommended. Alternatively, you may specify -DCMAKE_CXX_FLAGS="-march=x86-64-v3" to produce a more portable binary (only works on GCC≥10 and Clang≥12).

Usage

lrcaller [OPTIONS] "BAMFILE" "VCF_FILE_IN" "VCF_OUT_FILE"

For details, see lrcaller --help.

Citation

LRcaller is developed at deCODE Genetics by Bjarni V. Halldorsson, Doruk Beyter, Hannes Eggertson (@hannespetur) and Hannes Hauswedell (@h-2). Please cite the following research articel when using LRcaller in any academic work: https://doi.org/10.1038/s41588-021-00865-4