Welcome to the STOAT wiki!

Installation

STOAT can be installed on Linux or macOS. Follow the appropriate guide below to install the required dependencies and build STOAT:

NOTE: STOAT does not support static compilation (for now).

• Linux & macOS installation

Preparing the graphs

NOTE: STOAT does not support distance indexes built with versions of vg more recent than v1.69.0

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

Subcommands

1. Retrieve snarl genotypes.
   • stoat graph from the graph's embedded paths.
     • input: graph and indexes
     • output: snarl_genotypes.tsv.gz
   • stoat vcf from a VCF
     • input: VCF, graph, and indexes
     • intermediate file: snarl_info.tsv.gz
     • output: snarl_genotypes.tsv.gz
2. Test for association
   • stoat test
     • input: snarl_genotypes.tsv.gz
     • output: stoat.assoc.pvalues.tsv.gz
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.

Understanding the code

• Variation graph and snarls background
• Code overview
• Using the GBWT and r-index

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.