Bash and Snakemake pipelines for generating high-quality VQSR-filtered SNP and INDEL calls

Table of Contents

• BASH pipeline
• Snakemake pipeline (excerpt: read grooming and mapping)

BASH pipeline

1. run launch_filtering_mapping.sh - runs the initial checks and launches filtering_mapping_rawcalling.bsub (requires LSF system)
2. after all the bsub jobs are finished, run merge_UG.sh and genotypegvcf.sh
3. run ug_genotyping.bsub (requires LSF system)
4. after all bsub jobs are finished, run merge_UG1.sh
5. run filtering_vsqr.sh

Snakemake pipeline (excerpt: read grooming and mapping)

if on LSF cluster, launch as "sh scripts/submit_lsf.sh; adjust required and available resources in cluster.yaml

1. install conda (https://conda.io/projects/conda/en/latest/user-guide/install/index.html)
2. create conda environment (conda-env create --file environment.yaml)
3. activate conda environment (conda-env activate snakemake_read_vcf)
4. create data/ folder with required files (reference genome fasta; input fq.bz2 files)