Variant-aware Cas-OFFinder
==========================

**Variant-aware Cas-OFFinder** is a variant-aware potential off-target sites identifying tool 
based on Cas-OFFinder. Using a reference genome alone to search potential off-target sites
has many drawbacks since it may not contain individual variants, making it challenging for
therapeutic applications. VarCas-OFFinder considers individual variants along with 
reference genomes to search potential off-target sites. 

Quick Start to use the web interface
------------------------------------

1. Navigate to https://rgetoolkit.com/
2. Download the provided **Sample VCF file**
3. Default settings:

   - Target Genome: Homo sapiens (GRCh38/hg38)
   - PAM Type: SpCas9 from Streptococcus pyogenes: 5'-NRG-3'
   - Query Sequence: CAGCAACTCCAGGGGGCCGC
   - Mismatches: 3

4. Click Submit to process the sample file.
5. For custom analysis, upload your phased single-sample VCF file.







.. toctree::
   :maxdepth: 4
   :caption: Contents

   quickstart
   userguide
   version_history