dipdiff

This is a simple SV calling package for diploid assemblies. It uses a modified version of svim-asm. The package includes its own version minimap2 to ensure reproducibility between runs, as the result might be dependent on the aligner version and parameters.

Version 0.1

Installation & running

git clone https://github.com/fenderglass/dipdiff
cd dipdiff
git submodule update --init --recursive
make

Afterwards, you can execute:

./dipdiff.py

Output files

The output directory will contain variants.vcf file with structural variants.

Acknowledgements

The major parts of the dipdiff pipeline are:

• minimap2
• svim-asm

Authors

The pipeline was developed at UC Santa Cruz genomics institute, Benedict Paten's lab.

Main code contributors:

• Mikhail Kolmogorov

License

dipdiff is distributed under a BSD license. See the LICENSE file for details. Other software included in this discrubution is released under either MIT or BSD licenses.

How to get help

A preferred way report any problems or ask questions is the issue tracker.