insilicoSV generates synthetic diploid genome sequences, given a reference genome and a configuration file.
It supports the following functionality:
- 19 types of structural variants (simple and complex), indels, and SNPs
- a grammar to define custom structural rearrangement signatures
- random, context-aware (e.g., in repeat regions), or fixed-mode genome placement
Prerequisite: Python 3.8 and up - Install
Installation using pip:
$ pip install insilicosv
The recommended workflow for running insilicoSV is as follows:
- Create a new directory
- Populate a simulation config file and place it in the directory
- Run insilicoSV providing the config file as input:
insilicosv <config_yml>
- Results will be produced in this directory
The config file syntax is detailed in the Input guidelines section of the documentation.
For documentation outlining the different features of insilicoSV along with usage examples and data resources, please refer to the following sections:
Chris Rohlicek - crohlice@broadinstitute.org
Nick Jiang - nickj@berkeley.edu
Ilya Shlyakhter - ilya@broadinstitute.org
Victoria Popic - vpopic@broadinstitute.org
