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.
Installation & running
git clone https://github.com/fenderglass/dipdiff cd dipdiff git submodule update --init --recursive make
Afterwards, you can execute:
The output directory will contain
variants.vcf file with structural variants.
The major parts of the dipdiff pipeline are:
The pipeline was developed at UC Santa Cruz genomics institute, Benedict Paten’s lab.
Main code contributors:
- Mikhail Kolmogorov
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.