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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

• Retrieve snarl genotypes
  • stoat vcf from a VCF
  • stoat graph from the graph's embedded paths.
• Test for association: stoat test
• 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.