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The wiki holds documentation most relevant for develop. For information on a specific version of Truvari, see docs/

Citation:
English, A.C., Menon, V.K., Gibbs, R.A. et al. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol 23, 271 (2022). https://doi.org/10.1186/s13059-022-02840-6

Before you start

VCFs aren't always created with a strong adherence to the format's specification.

Truvari expects input VCFs to be valid so that it will only output valid VCFs.

We've developed a separate tool that runs multiple validation programs and standard VCF parsing libraries in order to validate a VCF.

Run this program over any VCFs that are giving Truvari trouble.

Furthermore, Truvari expects 'resolved' SVs (e.g. DEL/INS) and will not interpret BND signals across SVTYPEs (e.g. combining two BND lines to match a DEL call). A brief description of Truvari bench methodology is linked below.

Finally, Truvari does not handle multi-allelic VCF entries and as of v4.0 will throw an error if multi-allelics are encountered. Please use bcftools norm to split multi-allelic entries.

Index

• Updates
• Installation
• Truvari Commands:
  • anno
  • bench
  • collapse
  • consistency
  • divide
  • ga4gh
  • phab
  • refine
  • segment
  • stratify
  • vcf2df
• Development
• Citations