manninglab/metal repository overview

⁠METAL -- Meta analysis

⁠Description

This workflow performs a meta analysis of association results using the METAL software⁠

⁠Authors

This workflow is produced and maintained by the Manning Lab⁠. Contributing authors include:

• Tim Majarian ([email protected]⁠)
• Alisa Manning ([email protected]⁠).

⁠Dependencies

⁠Workflow execution

• WDL⁠
• Chromwell⁠

⁠METAL (included in Docker image)

• Metal - generic distribution⁠

⁠R packages

• data.table⁠
• qqman⁠

⁠Docker images

• Bioconductor⁠ - by Roby Joehanes ([email protected]⁠)
• METAL⁠

⁠Main Functions

⁠runMetal

This function generates the metal input script, processes each input results file, and runs the meta analysis

Inputs:

• assoc_files : an array of association results files, like those generated in the single variant association pipeline, must have a column labeled "MAF" (Array[File], .csv or .tsv)
• marker_column : column name in assoc_files with variant identifiers (string, default = snpID)
• sample_column : column name in assoc_files for weighting of variants (string, default = n)
• allele_effect_column : column name in assoc_files with effect allele (string, default = alt)
• allele_non_effect_column : column name in assoc_files with non effect allele (string, default = ref)
• pval_column : column in assoc_files with variant p-value (string, default = Score.pval)
• effect_column : column in assoc_files with variant effect (string, default = Score.Stat)
• out_pref : prefix for output filename (string)
• separator : character that separates each input result file (string, default = COMMA [WHITESPACE, TAB])
• analyze_arg : optional argument for other types of analyses (string, default = ZSCORE)

Outputs:

• result_file : results per variant for all variants tested (.TBL)
• metal_script : script that was generated as input to METAL (script.txt)
• log_file : log file capturing standard error of running METAL (.log)
• info_file : description of results_file columns, input files

⁠metalSummary

This function generates the metal input script, processes each input results file, and runs the meta analysis

Inputs:

• marker_column : column name in assoc_files with variant identifiers (string, default = snpID)
• pval_column : column in assoc_files with variant p-value (string, default = Score.pval)
• sample_column : column in assoc_files with number of samples (string, default = n)
• out_pref : prefix for output filename (string)
• metal_file : output of runMetal task (File)
• assoc_files : an array of association results files, like those generated in the

Outputs:

• csv : a comma separated file of results including METAL results and "cols_tokeep" from each input results file (.csv)
• plots : quantile-quantile and manhattan plots subset by MAF (all, <5%, >=5%) for meta-analysis p-values (.png)

⁠Other workflow inputs

• this_memory : amount of memory in GB for each execution of a task (int)
• this_disk : amount of disk space in GB to allot for each execution of a task (int)