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Welcome to the STOAT wiki!

Preparing the graphs

• graph conversion and indexing

Preparing the VCF for stoat vcf

More information about the genotyping pipeline and how to combine VCFs in the stoat vcf page.

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.