obelisc (Observational linkage scan) is an identical-by-descent (IBD) mapping tool based on the SNP streak approach.

obelisc is a command line tool to perform two effective nonparametric linkage analyses (i.e., SNP streak-based IBD mapping and runs of homozygosity (ROH) mapping). obelisc also supports an intuitive visualization of the analytical results.

obelisc requires no predefined inheritance model with parameters and is applicable to both dominant and recessive traits.

If you use Obelisc or any material in this repository, please cite

Sonehara K and Okada Y. Obelisc: an identical-by-descent mapping tool based on SNP streak. Bioinformatics, 2020.

• python 3.x
• numpy
• pandas
• matplotlib
• pysnptools
• argparse
• Cython (if you want to build LOCH_MappingTools from cython code)

obelisc can be installed using pip.

pip3 install git+https://github.com/qsonehara/Obelisc

When you install obelisc, you get a simple command-line interface. You can perform SNP streak-based IBD mapping and ROH mapping by running the command obelisc as follows:

obelisc example

Here, example is the prefix of a PLINK binary fileset (i.e., example.fam, example.bim, and example.bed) and a text file specifying case individuals (i.e., example.case).

You can run obelisc with the example dataset provided as follows:

obelisc hapmap3_r2_b37_fwd.consensus.qc.poly.JPT.example

You can specify the filename of another case-specifying text file, the size of the scanning window, the minimum size of output stretches, the filename of mapping output, and the filename of the diagram of results as follows;

obelisc example -c case_file.case -w 1500 -s 1500 -o example_ibdmapping -f example_out.pdf

Kyuto Sonehara ([email protected])