gwas-report.md

gwas-report

Create interactive html reports from GWAS summary statistics

Plot results from regenie

Create a html report from file regenie.txt.gz and store output in regenie.report.html:

java -jar genomic-utils.jar gwas-report \
  regenie.txt.gz \
  --output regenie.report.html

If the columns in your file are different from regenie, you could set them manually:

java -jar genomic-utils.jar gwas-report \
  regenie.txt.gz \
  --chr CHROM \
  --pos GENPOS \
  --pval LOG10P \
  --output regenie.report.html

Annotate top hits

You could use the annotate command to annotate results from regenie with rsids to use this information in summary table and manhattan plot:

java -jar genomic-utils.jar gwas-report \
  regenie.annotated.txt.gz \
  --chr CHROM \
  --pos GENPOS \
  --pval LOG10P \
  --rsid RSID \
  --ref REF \
  --alt ALT \
  --beta BETA \
  --annotation TOP_HIT \
  --output regenie.report.html

You could use --gene to define which column contains the gene name and --anotation GENE to show it in the plot:

java -jar genomic-utils.jar gwas-report \
  regenie.annotated.txt.gz \
  --chr CHROM \
  --pos GENPOS \
  --pval LOG10P \
  --rsid RSID \
  --ref REF \
  --alt ALT \
  --beta BETA \
  --gene NEAREST_GENE \
  --annotation TOP_HIT \
  --output regenie.report.html

Create csv file with binned infos

Bins variants in regenie.txt.gz and store binned infos in regenie.report.txt. This file could be used to create plots for publications.

java -jar genomic-utils.jar gwas-report \
  regenie.txt.gz \
  --chr CHROM \
  --pos GENPOS \
  --pval LOG10P \
  --format CSV \
  --output regenie.report.txt
``