Vcfstats is a tool that can generate metrics from a vcf file.

  • General stats (default, can be disabled)
  • Genotype stats (default, can be disabled)
  • Sample compare (default, can be disabled)
  • Sample distributions (default, can be disabled)
  • Field histograms

This tool can run locally single threaded but also on a Apache Spark cluster.


For documentation and manuals visit our page.


VcfStats is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.


For any question related to VcfStats, please use the github issue tracker or contact the SASC team directly at: [email protected].