Commandline Parameters

Users can specify the following parameters when running the Nextflow pipeline

--ancestry

This parameter is used to specify the ancestry group to perform the analysis on. Valid values for this parameter are ['EUR', 'SAS', ...]

--assembly

This parameter is used to specify the genome assembly of the input genotyping files. The outputs of the pipeline will all be in relation to hg38. If you supply genotypes from a different reference assembly specify one of the following options ['hg18', 'hg19'] so the positions can be lifted over to hg38. The default value is 'hg38'

--covarfile

This parameter is used to specify the path of the covariates to include in the model. Each subject to include in the analysis needs to have their own covariates. For more details, see the page on file inputs to the pipeline.

--covariates

This parameter is used to specify the covariates to include in the model from the input covariates file and the genetic principle componenets from the ancestry steps. This paraemeter should be populated with a space delimited string of the column names to include in the model from the --covarfile option. By default the model is fit with "SEX PC1 PC2 PC3"

--dataset

This parameter is used to specify an identifier for the input genotype files so that subsequent re-runs of the pipeline can use cached results from the variant filtering and ancestry + outlier detection steps. The default value is '' and it is highly recommended to set this parameter to avoid misusing cached results.

--input_vcf

This parameter is used to specify the paths of the genotyping files. The pipeline requires genotypes in uncompressed (*.vcf) or compressed (*.vcf.gz) files. Genotype files should be shredded at the chromosome level and each file should contain the chromosome number prefix with 'chr' case insensitive.

Note: The inclusion of wildcard (*) in the path requires the use of quotes

Acceptable filenames

--input_vcf "/path/to/dataset_prefix_chr*.vcf"
--input_vcf "/path/to/dataset_chr*_suffix.vcf.gz"
--input_vcf "/path/to/chr*.vcf"

--kinship

This parameter specifies the relatedness level to filter against from the pairwise kinship between subjects. By default this value is "0.177" to filter out first-degree relations.

--longitudinal_flag

This flag is used to specify the estimation of longitudinal associations via the GALLOP algorithm. If the option is not supplied then the pipeline performs a cross-sectional GWAS using plink2.

Note: performing longitudinal analysis requires the inclusion of a study_days variable in the input phenotype. This variable should correspond to the timepoint (in days) since the start of the study at which the measurement for the outcome was taken. Initial measurements taken at baseline will have a study_days of 0.

--model

This parameter can be used to specify a custom model with higher order terms when the --longitudinal_flag is invoked. To include higher order terms in the cross-sectional analysis, include them as a column in the --covarfile and declare them in the --covariates parameter.

--out

This parameter is used to specify the output suffix of the files to distinguish results or re-runs of the pipeline.

--phenofile

This parameter is used to specify the path of the outcome file to do the association on. For cross-sectional analysis, the pipeline expects data to be formatted in at least 2 columns, IID and y

For longitudinal-analysis, a third column study_days represents the timepoint in the study that the observation was taken. This variable should be in given in relation to the number of days since the baseline observation was taken in the study.

--pheno_name

This parameter can be used to specify the column in the --phenofile containing the outcome of interest. If multiple outcome are present or if the column with the outcome does not have the header y

--r2thres

This parameter is used to filter out imputed geneotypes of low quality if the input genotyping files include imputed variants.