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(Work in progress.. some links may not work.. Some details may be missing)

Before you start

VCFs aren't always created with a strong adherence to the format's specification. To make matters worse, many tools don't require input VCFs to strictly adhere to the format.

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 before opening a ticket.

Index:

• Updates
• Truvari Commands:
  • bench
    • The multimatch parameter
    • Edit Distance Ratio vs Sequence Similarity
    • Multi-allelic VCFs
    • stratifications.sh
    • Comparing two SV programs
  • stats
  • consistency
  • anno
    • Creating an annotation source