Description

Run bivariate REML analysis with a single dense GRM

Input

name:type
description
pattern

meta

:map

Groovy map containing dense GRM metadata meta.id must be the GRM basename passed to --grm (for example plink_simulated_dense for plink_simulated_dense.grm.{id,bin,N.bin})

grm_files

:file

Dense GRM bundle containing sample identifier, binary matrix, and sample-count matrix files

*.grm.*

meta2

:map

Groovy map containing phenotype file metadata for the same analysis unit as the primary GRM metadata e.g. [ id:'plink_simulated_dense' ]

phenotype_file

:file

Shared bivariate phenotype file passed to --pheno

*.{phe,pheno,txt,tsv}

phenotype_col1

:integer

First phenotype column passed to --reml-bivar (for example 1). Pass an empty value together with phenotype_col2 to use GCTA’s default bivariate phenotype columns.

phenotype_col2

:integer

Second phenotype column passed to --reml-bivar (for example 2). Pass an empty value together with phenotype_col1 to use GCTA’s default bivariate phenotype columns.

meta3

:map

Groovy map containing quantitative covariate metadata for the same analysis unit as the primary GRM metadata e.g. [ id:'plink_simulated_dense' ]

quant_covariates_file

:file

Quantitative covariates file, pass [] when absent

*.{covar,cov,txt,tsv}

meta4

:map

Groovy map containing categorical covariate metadata for the same analysis unit as the primary GRM metadata e.g. [ id:'plink_simulated_dense' ]

cat_covariates_file

:file

Categorical covariates file, pass [] when absent

*.{covar,cov,txt,tsv}

Output

name:type
description
pattern

bivariate_results

meta

:map

Groovy map containing dense GRM metadata meta.id is used as the default output prefix

*.hsq

:file

Bivariate REML result file

*.{hsq}

log_file

meta

:map

Groovy map containing dense GRM metadata meta.id is used as the default output prefix

*.log

:file

Bivariate REML log file

*.{log}

versions_gcta

${task.process}

:string

The process the version was collected from

gcta

:string

The tool name

gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\1/p'

:eval

The command used to retrieve the GCTA version

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the version was collected from

gcta

:string

The tool name

gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\1/p'

:eval

The command used to retrieve the GCTA version

Tools

gcta
GPL-3.0-only

Genome-wide Complex Trait Analysis (GCTA) estimates genetic relationships, variance components, and association statistics from genome-wide data.

yanglab.westlake.edu.cn/software/gcta yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf https://yanglab.westlake.edu.cn/software/gcta/
included in
gwas
maintainer
Github user lyh970817
get in touch
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