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

Afterwards, you can execute:


Output files

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.


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