---
name: "scoary"
section: "1"
platform: "linux"
package: "scoary"
version: "1.6.16-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/scoary"
---

# scoary(1)

pangenome-wide association studies

## NAME

scoary - pangenome-wide association studies

## SYNOPSIS

scoary \[-h\] \[-t TRAITS\] \[-g GENES\] \[-n NEWICKTREE\] \[-s START\_COL\] \[--delimiter DELIMITER\] \[-r RESTRICT\_TO\] \[-o OUTDIR\] \[-u\] \[-p P\_VALUE\_CUTOFF \[P\_VALUE\_CUTOFF ...\]\] \[-c \[{I,B,BH,PW,EPW,P} \[{I,B,BH,PW,EPW,P} ...\]\]\] \[-m MAX\_HITS\] \[--include\_input\_columns GRABCOLS\] \[-w\] \[--no-time\] \[-e PERMUTE\] \[--no\_pairwise\] \[--collapse\] \[--threads THREADS\] \[--test\] \[--citation\] \[--version\]

## OPTIONS

### optional arguments:

- **-h**, **--help**

  show this help message and exit

### Input options:

- **-t** TRAITS, **--traits** TRAITS

  Input trait table (comma-separated-values). Trait presence is indicated by 1, trait absence by 0. Assumes strain names in the first column and trait names in the first row

- **-g** GENES, **--genes** GENES

  Input gene presence/absence table (comma-separatedvalues) from ROARY. Strain names must be equal to those in the trait table

- **-n** NEWICKTREE, **--newicktree** NEWICKTREE

  Supply a custom tree (Newick format) for phylogenetic analyses instead instead of calculating it internally.

- **-s** START\_COL, **--start\_col** START\_COL

  On which column in the gene presence/absence file do individual strain info start. Default=15. (1-based indexing)

- **--delimiter** DELIMITER

  The delimiter between cells in the gene presence/absence and trait files, as well as the output file.

- **-r** RESTRICT\_TO, **--restrict\_to** RESTRICT\_TO

  Use if you only want to analyze a subset of your strains. Scoary will read the provided comma-separated table of strains and restrict analyzes to these.

### Output options:

- **-o** OUTDIR, **--outdir** OUTDIR

  Directory to place output files. Default = .

- **-u**, **--upgma\_tree**

  This flag will cause Scoary to write the calculated UPGMA tree to a newick file

- **-p** P\_VALUE\_CUTOFF \[P\_VALUE\_CUTOFF ...\], **--p\_value\_cutoff** P\_VALUE\_CUTOFF \[P\_VALUE\_CUTOFF ...\]

  P-value cut-off / alpha level. For Fishers, Bonferronis, and Benjamini-Hochbergs tests, SCOARY will not report genes with higher p-values than this. For empirical p-values, this is treated as an alpha level instead. I.e. 0.02 will filter all genes except the lower and upper percentile from this test. Run with "-p 1.0" to report all genes. Accepts standard form (e.g. 1E-8). Provide a single value (applied to all) or exactly as many values as correction criteria and in corresponding order. (See example under correction). Default = 0.05

- **-c** \[{I,B,BH,PW,EPW,P} \[{I,B,BH,PW,EPW,P} ...\]\], **--correction** \[{I,B,BH,PW,EPW,P} \[{I,B,BH,PW,EPW,P} ...\]\]

  Apply the indicated filtration measure. Allowed values are I, B, BH, PW, EPW, P. I=Individual (naive) p-value. B=Bonferroni adjusted p-value. BH=BenjaminiHochberg adjusted p. PW=Best (lowest) pairwise comparison. EPW=Entire range of pairwise comparison p-values. P=Empirical p-value from permutations. You can enter as many correction criteria as you would like. These will be associated with the p\_value\_cutoffs you enter. For example "-c I EPW **-p** 0.1 0.05" will apply the following cutoffs: Naive p-value must be lower than 0.1 AND the entire range of pairwise comparison values are below 0.05 for this gene. Note that the empirical p-values should be interpreted at both tails. Therefore, running "-c P **-p** 0.05" will apply an alpha of 0.05 to the empirical (permuted) p-values, i.e. it will filter everything except the upper and lower 2.5 percent of the distribution. Default = Individual p-value. (I)

- **-m** MAX\_HITS, **--max\_hits** MAX\_HITS

  Maximum number of hits to report. SCOARY will only report the top max\_hits results per trait

- **--include\_input\_columns** GRABCOLS

  Grab columns from the input Roary file. and puts them in the output. Handles comma and ranges, e.g. **--include\_input\_columns** 4,6,8,16-23. The special keyword ALL will include all relevant input columns in the output

- **-w**, **--write\_reduced**

  Use with **-r** if you want Scoary to create a new gene presence absence file from your reduced set of isolates. Note: Columns 1-14 (No. sequences, Avg group size nuc etc) in this file do not reflect the reduced dataset. These are taken from the full dataset.

- **--no-time**

  Output file in the form TRAIT.results.csv, instead of TRAIT\_TIMESTAMP.csv. When used with the **-w** argument will output a reduced gene matrix in the form gene\_presence\_absence\_reduced.csv rather than gene\_presence\_absence\_reduced\_TIMESTAMP.csv

### Analysis options:

- **-e** PERMUTE, **--permute** PERMUTE

  Perform N number of permutations of the significant results post-analysis. Each permutation will do a label switching of the phenotype and a new p-value is calculated according to this new dataset. After all N permutations are completed, the results are ordered in ascending order, and the percentile of the original result in the permuted p-value distribution is reported.

- **--no\_pairwise**

  Do not perform pairwise comparisons. Inthis mode, Scoary will perform population structure-naive calculations only. (Fishers test, ORs etc). Useful for summary operations and exploring sets. (Genes unique in groups, intersections etc) but not causal analyses.

- **--collapse**

  Add this to collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units.

### Misc options:

- **--threads** THREADS

  Number of threads to use. Default = 1

- **--test**

  Run Scoary on the test set in exampledata, overriding all other parameters.

- **--citation**

  Show citation information, and exit.

- **--version**

  Display Scoary version, and exit.

by Ola Brynildsrud (olbb@fhi.no)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.