vmgiang/skin-paper

This script is to generate a raw report folder ready for System group.

Requirements:

• R version: R version 4.1.1
• Packages for R:
  • data.table
  • dplyr
• Plink 1.9 : https://www.cog-genomics.org/plink/

INPUT:

* Imputed vcf file

OUTPUT:

* Raw reports for all samples in vcf files : 

	* histogram*.pdf
	
	* histogram_points*.pdf

	* summary*.csv

	* traitDetailM*.csv

	* traitM*.csv   

CHECKING Quality of Raw report:

* Rscript quality_check.R path_to_raw_report

RUNNING STEPS:

1. Edit parameters in src/parameters.sh:

   • MAF_thres : MAF threshold

   • IMP_thres : Imputation threshold

   • hwe : Hardy-weiberg

2. Run pipeline for generating report :

   ./run_pipline.sh basedir_path basepop_prefix tardir_path tarpop_prefix outdir_path db_report

   • basedir_path : GWAS summary statistic, Clumped SNPs from vn1008

   • basepop : prefix Gwas sumstat

   • tardir_path : vcf_file directory contains imputed VCF file

   • tarpop_prefix : prefix of vcf files ($tarpop_prefix.vcf.gz)

   • db_report : db for generating report