blokadniki

This repository is dedicated to GWAS analysis of the genomes of people who survived the Siege of Leningrad.

What is this project about?

What's in this repository?

Paired-end sequencing data processing pipline.

A Snakemake workflow to process cohort samples related individuals of paired-end sequencing data (WGS or WES) using bwa and GATK4. Quality control checks are also undertaken with fastp.

This workflow is designed to follow the GATK best practice workflow for germline short variant discovery (SNPs + Indels), taking the data from fastq to annotated vcf (raw sequencing data to annotated called variants).

1. Raw read QC (Fastp)
2. Alignment against reference genome (Burrows-Wheeler Aligner)
3. Mark duplicates (GATK MarkDuplicates)
4. Base recalibration (GATK BaseRecalibrator and GATK ApplyBQSR)
5. Haplotype calling (GATK HaplotypeCalller)
6. Combine GVCF into multi-sample GVCF (GATK GenomicsDBImport)
7. Genotyping (GATK GenotypeGVCFs)
8. Annotation (GATK Funcotator)

Main output files.

• results/raw_joint_cohort.vcf
• results/raw_joint_cohort_annotated.vcf

Prerequisite

Prerequisite software and environment can be found in pipeline_run_env.yaml