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 github.io 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 BIOPET pipelines.