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Confluence Workflows and Tools

Available Workflows

regenie workflow for GWAS

We have forked and modified the nf-gwas nextflow workflow for Confluence analysis. It's on Confluence GitHub at https://github.com/confluence-breast-cancer-consortia/nf-gwas. The release with tag confluence-v0.1 was imported to the confluence-concept-1-analyses project in DNAnexus as an applet. Please note that the base Docker image for the nf-gwas workflow was also modified and is hosted here under the Confluence GitHub packages.

Below is a sample command line for running the nf-gwas workflow on DNAnexus. This requires using dx-toolkit on your local computer. Please refer to the dx-toolkit section under Demo to learn how to use dx-toolkit. 

dx run applet-J3264V04kqq6GZKYYbB4jY58 \
    -i nextflow_run_opts="-profile docker -queue-size 250" \
    -i outdir=<output_directory_name> \
    -i preserve_cache=true \
    -i nextflow_soft_confs=/tools/nf-gwas-applet/configs/2cpuForStep2_loocv_report.config \
    -i nextflow_pipeline_params="--project <uniqueNameForYourProject> \
    --container ghcr.io/confluence-breast-cancer-consortia/nf-gwas:regenie4.1-bgenix \
    --genotypes_prediction_bed dx://project-<project_id>:/<path_to_genotype_bed_file> \
    --genotypes_prediction_bim dx://project-<project_id>:/<path_to_genotype_bim_file> \
    --genotypes_prediction_fam dx://project-<project_id>:/<path_to_genotype_fam_file> \
    --genotypes_association dx://project-<project_id>:/<path_to_imputed_data>/chr*/*.bgen \
    --regenie_sample_file dx://project-<project_id>:/<path_to_one_of_the_bgen.samples_file> \
    --association_build hg38 --genotypes_association_format bgen \
    --phenotypes_filename dx://project-<project_id>:/<path_to_phenotype_file> \
    --phenotypes_columns BreastCancer --phenotypes_binary_trait true \
    --covariates_filename dx://project-<project_id>:/<path_to_covariates_file> \
    --covariates_columns PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10 --regenie_test additive --prune_enabled true \
    --prune_maf 0.05 --qc_maf 0.02 --qc_mac 0 --qc_geno 0.05 --qc_hwe 0 --qc_mind 0.05 --prune_r2_threshold 0.9 --regenie_min_mac 30 \
    --regenie_min_imputation_score 0.2 --annotation_min_log10p 2 \
    --rsids_filename dx://project-GzJXf184kqq1512KkxGJ6f3Y:/data-annotation/rsids-v154-hg38.index.gz" \
    --destination project-GzJXf184kqq1512KkxGJ6f3Y:/<directory_on_dnanexus>/ --brief -y

Available Tools

rstudio with gwas tools

We have updated the R Studio Docker image to be used on DNAnexus here. The DockerFile is here. Please feel free to modify this or create your own Docker image to be used on DNAnexus.

Below is an example of using the docker image with swiss-army-knife to plot manhatten and qq plots using an R script.

dx run app-swiss-army-knife \
   -iimage="ghcr.io/confluence-breast-cancer-consortia/rstudio_with_gwas_tools:v1.0" \
   -iin=tools/scripts/manhattan_qq_plot.R \
   -iin=<project_name>:<path_to_summary_stat_file> \
   -icmd="Rscript manhattan_qq_plot.R --input_file <summary_stat_file> --outdir <output_directory> --num_cases <num_cases> --num_controls <num_controls>" \
   --destination <project_name>:/<output_directory_on_dnanexus> -y

Identify Independent GWAS loci

We have an R script that carries out Greedy forward selection of independent GWAS loci based on distance, R², and D' criteria. Please see the README file for more information on how to run it on a slurm cluster or how to build your own DNAnexus app. For Confluence Concept 1 analysis. The DNAnexus applet can be found under the tools directory.

For example, if you want to run the algorithm for the pooled analysis, you can launch the job on your computer by running the following command, where - sigres_file: significant results file - ref_bim: reference panel bim - ld_file: pre-computed LD file - metaltype: Pooled/afr/amr/eur/eas

dx run /tools/identify_independent_loci \
  -isigres_file=/ref/Mar20sigres.txt \
  -iref_bim=/ref/merged_ref.bim \
  -ild_file=/ref/Mar20.ld_pairs_5mb.ld \ 
  -imetaltype=Pooled \
  -ioutprefix=Mar30 \
  --priority high \
  --destination <project_name>:/<output_directory_on_dnanexus> \
  -y

When you click on it, you will see this interface. you can click to fill in the input files to run the applet. We recommend using priority high to run the applet, as it could run for several hours. Using high priority will prevent it from getting killed halfway.

Support

For questions or issues with Confluence workflows and tools, please use the relevant issues and discussions on Confluence GitHub repositories.