Genotype Comparison Pipeline

Introduction

This repository contains a Bash pipeline for comparing genotypes between Whole Genome Sequencing (WGS) and SNP-CHIP datasets. The pipeline is designed to be used in a Linux environment.

Clone the repository:

git clone https://github.com/MBHZG2/ngs_geno_comparison.git cd ngs_geno_comparison

Update the configuration file config.txt with the appropriate inputs and tools path

Run the Pipeline

Usage

to run

bash PiP_GENO_NGS_COM_compined.run.sh -c $sample_config_file.txt

Step1 generate config file for each sample

bash generate.conf.for.call.sh

Step 2: Run the variant calling script

sh call.sh -B "$BCFTOOLS_PATH" -P "$PLINK_PATH" -O "$OUTPUT_DIR" -I "$BAM_PATH" -S "$WGS_SAMPLE" -R "$REF_PATH" -N "$SNP_POS_FILE"

Step 3: Run the comparison script

sh Comparison_GENOTYPE_WGS_SNP_CHIP.sh -W "$WGS_SAMPLE" -G "$GENOT_SAMPLE_ID" -O "$OUTPUT_DIR" -I "$input_genotype_tepd_file" -i "$input_WGS_tepd_file" -m "$PLINK_MAP_FILE"