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vtc website  

The Variant Tool Chest (VTC) is designed to be a tool chest for analyzing variants (particularly VCF files) and to be easily extensible. We hope you will incorporate your valuable tools/algorithms to VTC. These tools/algorithms may be independently published or not. In either case, we want to build a well-integrated tool chest. Please see our BMC Bioinformatics paper. VTC is still under development and we are working to improve features and reliability, but there are several specific gaps VTC currently fills including:

Advanced, genotype-aware set operations Simple VCF comparisons Variant summaries (detailed and minimal) Variant statistics (e.g. association studies) There are currently two tools in VTC known as SetOperator and VarStats. VarStats is still under development but currently performs association analyses on single or multi-sample VCFs and will print out detailed VCF summaries.

Environment Modules

Run module spider vtc to find out what environment modules are available for this application.

System Variables

  • HPC_VTC_DIR - installation directory