SVELDT is a bioinformatic tool that refines structural variations(SV) using long-read analysis
SVELDT is written in C++ and uses htslib library written in C. Please first install and compile htslib. Instructions are given below.
Please visit htslib repository for detailed instructions.
You need to first clone htslib and its submodule htscodecs. Please run the following command inside the cloned repository of SVELDT.
git submodule update --init --recursive
Then, go to the htslib directory to compile the library.
cd htslib
./configure
make
make install
The official installation documentation suggest to rum ./configure command if you need optional functionality to be enabled. If not, you can skip the command.
The default installation directory of libraries, library header files, utilities, several manual pages, and a pkgconfig is /usr/local. This might cause permission errors if you installed the htslib in machines where you do not own the root privilege. Also, this configuration installs the library globally, but, you can change the directory by running the following command
# instead of
make install
# run
make prefix=DIR install
Minimal installation of htslib is
cd htslib
make install
If after these, you should have installed and compiled htslib. If you encounter any error, please visit htslib and try to follow the instructions there. Now, you need to compile SVELDT. To do this please run the following commands
cd .. # You need to go SVELDT directory
make
Great, now you can use the program by running
./sveldt --bam bam_file --vcf vcf_file
where bam_file, vcf_file and output_file_name are the input files.