iGenVar

The official repository for the iGenVar project.

Installation

Instructions:

1. clone this repository: git clone --recurse-submodules https://github.com/seqan/iGenVar.git or git clone https://github.com/seqan/iGenVar.git and fetch the seqan3 submodule after cloning: git submodule update --recursive --init
2. create a build directory and visit it: mkdir build && cd build
3. run cmake: cmake ../iGenVar
4. build the application: make
5. optional: build and run the tests: make test or ctest
6. optional: build the api documentation: make doc
7. execute the app: ./bin/iGenVar

(Built using the SeqAn3 App Template)

We created small examples, which you can use to test our app: ./bin/iGenVar -i ./test/data/paired_end_short_read_mini_example.sam -j ./test/data/single_end_mini_example.sam -o ./test/data/output.vcf --method cigar_string --method split_read --min_var_length 5