---
name: "trinculo"
section: "1"
platform: "linux"
package: "trinculo"
version: "0.96+dfsg-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/trinculo"
---

# trinculo(1)

toolkit to carry out genetic association for multi-category phenotypes

## NAME

trinculo - toolkit to carry out genetic association for multi-category phenotypes

## DESCRIPTION

Running a multinomial logistic analysis

### Usage:

- trinculo MODE

  \[--bfile GENOTYPES\_PREFIX \| **--dosage** GENOTYPES.DOSE \] \[--out OUTPUT\_PREFIX\] **--pheno** PHENOTYPES.TXT **--phenoname** PHENOTYPE \[--basepheno REF **--missingpheno** MISSING \] \[--covar COVARIATES.TXT **--normalize\]** \[--condition SNPS.TXT\] \[--priors PRIORS.TXT \| **--defaultprior** **--priorsigma** PRIORVAR **--priorcor** PRIORCOR **--covarsigma** PRIORVAR \| **--empiricalprior**  \] \[ **--select** **--phenops** **--errormat** **--fullmodel** **--waldstats** \] \[ **--noassoc** \] \[--threads n\] \[ **--precision** DIGITS \] \[ **--fitIter** NITER **--fitAbsTol** ABSTOL **--fitRelTol** RELTOL \] \[--help\]

## OPTIONS

MODE    - Either multinom or ordinal for multinomial or ordinal logistic regression

**--bfile** FILE\_PREFIX     - Genotype input in binary plink format (FILE\_PREFIX.bed, FILE\_PREFIX.bim and FILE\_PREFIX.fam) **--dosage** FILE   - Genotype input in dosage format **--out** PREFIX    - The prefix used for output files \[default is "trinculo"\]

**--pheno** FILE    - Phenotype input (same format as plink)--phenoname STRING      **-The** phenotype in the phenotype file to analyse **--basepheno** STRING      - The reference category to use for the multinomial analysis \[defaults to first category encountered\] **--missingpheno** STRING   - The symbol to be use to indicate a missing phenotype in the phenotype file

**--condition** FILE        - A file containing a list of SNPs (one per line) to conditon on (i.e. include as covariates)

**--covar** FILE    - A file containing covariates to condition on (same format as plink) **--normalize**     - Normalizes covariates to have a variance of 1 \[off by default\]

**--priors** FILE   - A prior covariance matrix on effect sizes **--defaultpriors** - Construct a prior matrix based on default values **--priorsigma** VALUE      - Set the prior variance on effect sizes within a disease\[default is 0.04\] **--priorcor** VALUE        - Set the prior correlation on effect sizes across diseases \[default is 0\] **--covarsigma** VALUE      - Prior on the covariate effect size \[Default is 1\] **--empiricalprior**         - Calculate an empirical prior directly from the data **--noassoc**       **-do** not do any association testing, just infer the prior

**--select**        **-Do** Bayesian model selection (i.e. calculate marginal likelihoods for each sharing model) **--phenops**       **-Do** a likelihood ratio test on each phenotype individually **--waldstats**     **-Calculate** standard errors, Z scores and Wald p-values **--errormat**      **-Output** the variance-covariance matrix for the log odds ratio **--fullmodel**     **-Output** all parameter estimates and the full error matrix

**--threads** n     Use up to n cores

**--precision** DIGITS      Print output to DIGITS significant figures

**--fitIter** NITER Try up to NITER iterations when fitting models **--fitAbsTol** ABSTOL      Terminate model fitting if results change by less than ABSTOL **--fitRelTol** RELTOL      Terminate model fitting if results change by less than (RELTOL x value)

**--help**  - Prints this message

## AUTHOR

 This manpage was written by Pranav Ballaney for the Debian distribution and\
  can be used for any other usage of the program.