Create interactive html reports from GWAS summary statistics
This script is now part of genomic-utils.
- Download gwas-report.jar from releases
- Validate installation with
java -jar gwas-report.jar version
Create a html report from file regenie.txt.gz
and store output in regenie.report.html
:
java -jar gwas-report.jar report \
--input regenie.txt.gz \
--output regenie.report.html
If the columns in your file are different from regenie, you could set them manually:
java -jar gwas-report.jar report \
--input regenie.txt.gz \
--chr CHROM \
--pos GENPOS \
--pval LOG10P \
--output regenie.report.html
You could use tabix-merge to annotate results from regenie with rsids to use this information in summary table and manhattan plot:
java -jar gwas-report.jar report \
--input 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 gwas-report.jar report \
--input 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
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 gwas-report.jar report \
--input regenie.txt.gz \
--chr CHROM \
--pos GENPOS \
--pval LOG10P \
--format CSV \
--output regenie.report.txt
gwas-report
is MIT Licensed.