stoat graph - Pa-Tou/stoat GitHub Wiki

The stoat graph subcommand retrieves the genotypes of the haplotype paths of a graph, for each snarl in the pangenome. The input is a variation graph with haplotype paths. Within each snarl, paths are partitioned based on the walk they take through the snarl.

After running stoat graph, see how to run stoat test to perform the test between snarls and a phenotype.

Preparing the graph

stoat graph takes as input a variation graph, a distance index, and (optionally) an r-index. The variation graph can be in .hg, .pg, or .gbz format (from libbdsg and gbwtgraph). If the variation graph is in .gbz format, it is highly recommended to use an r-index as this will speed up the computation considerably. Instructions for converting between graph formats and building the distance index can be found here.

Running stoat graph

The base command for retrieving the snarls genotypes is:

stoat graph --graph <graph.hg> --distance-index <graph.dist> -o <output_directory>

Reference paths

The reference paths specified by --reference-file and/or --reference-prefix will be used for specifying coordinates of the variants. If reference paths were not specified (or did not traverse a given snarl), then reference-sense paths will be used. If neither are present, then any sample that traversed the variant may be used as reference path.

Output

The output is written to a file snarl_genotypes.tsv.gz in the specified output directory. The tsv output contains one locus per line. The format is described here.

stoat graph full list of arguments

Stoat v0.0.4
Usage: stoat graph -g [graph] -d [distance index] [options]
Retrieves snarl genotypes based on the haplotype paths present in the graph
Output: snarl_genotypes.tsv.gz written to the specified output directory

input:
  -g, --graph FILE                   Use this graph (required)
  -G, --r-index FILE                 Use this r-index (recommended, requires -g be a gbz)
  -d, --distance-index FILE          Use this distance index

output:
  -o, --output DIR                   Output directory name [stoat_output]
  -L, --find-alleles                 Find the walks and lengths of alleles (they will be "." without this flag). This is slow if not using the r-index.
  -u, --no-bgzip                     Don't compress the output file with bgzip

options:
  -t, --threads N                    Number of threads to use
  -V, --verbose INT                  Verbosity level (0=error, 1=warn, 2=info, 3=debug, 4=trace)
  -l, --allele-size-limit INT        Don't report variants smaller than this [0]
  -R, --reference-file FILE          Path to the reference file, one path name per line.
  -r, --reference-prefix NAME        The prefix of paths to be used as references.
                                     If references are not given, use any reference-sense paths in the graph. Check paths with vg paths -M
  -a, --ascii                        Print the STOAT ascii art banner
  -h, --help                         Print this help message
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