Free NGS utilities

RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats.


Key Features

  • Accurately perform call set comparison
  • Mendelian consistency analysis
  • VCF filtering, merging, annotation
  • FASTA/FASTQ, SAM/BAM, BED, PED manipulation
  • Suite of NGS simulation tools
  • BSD Licensed source code on github

Over the years one of the more valuable tools we've developed for internal testing and development purposes is an accurate and efficient way to compare genotypes from multiple VCFs for a set of individuals. In particular, our tool, vcfeval, is capable of dealing with differences in representation that can arise in complex situations or when comparing variants produced by different callers (more details are in this presentation on slideshare or this detailed publication). To date, no other tool is capable of performing this analysis as accurately as RTG vcfeval. Through our collaborations we have found this tool to be highly useful outside of RTG and have been asked to make it more widely available.

One of our core values is giving back to the community, so we have put the utilities for VCF comparison, filtering, and other manipulation that are found in our other products into RTG Tools, which we are making freely available. As well as the precompiled packages below, source code is available on github under the Simplified BSD License.

If you have any problems or questions, there is now a general discussion group that you may wish to join and an announcements only group where you can be notified of new releases.


The current version of RTG Tools is 3.12.1


Download RTG Tools For Linux

Download RTG Tools for Mac (No JRE)

Download RTG Tools for Windows


Also available are some supporting datasets such as pre-formatted human reference and metagenomic reference datasets.