Table of Contents
- run launch_filtering_mapping.sh - runs the initial checks and launches filtering_mapping_rawcalling.bsub (requires LSF system)
- after all the bsub jobs are finished, run merge_UG.sh and genotypegvcf.sh
- run ug_genotyping.bsub (requires LSF system)
- after all bsub jobs are finished, run merge_UG1.sh
- run filtering_vsqr.sh
if on LSF cluster, launch as "sh scripts/submit_lsf.sh; adjust required and available resources in cluster.yaml
- install conda (https://conda.io/projects/conda/en/latest/user-guide/install/index.html)
- create conda environment (conda-env create --file environment.yaml)
- activate conda environment (conda-env activate snakemake_read_vcf)
- create data/ folder with required files (reference genome fasta; input fq.bz2 files)