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Welcome to the STOAT wiki!

Preparing the graphs

• graph conversion and indexing
• generating the VCF input for stoat vcf

Subcommands

1. Retrieve snarl genotypes
   • stoat vcf from a VCF
   • stoat graph from the graph's embedded paths.
2. Test for association: stoat test
3. Post-processing
   • stoat BHcorrect corrects for multiple testing using Benjamini-Hochberg.
   • stoat change-ref changes the reference paths used in STOAT's output without having to rerun genotyping and testing.

Next?

• Page explaining the netgraph representation and how we write allele traversal through netgraphs.
• FAQ?
  • Difference between stoat graph and stoat vcf.
  • Using other snarl definitions.
  • Using other pangenome genotypers.