GitHub - vibaotram/gbp_variantcalling: My SNP calling pipeline following GATK best practice for Germline short variant discovery

My SNP calling pipeline from fastq files to a single analysis-ready VCF

snakemake gbp_variantcalling --use-conda

Name		Name	Last commit message	Last commit date
Latest commit History 81 Commits
.Rhistory		.Rhistory
.gitignore		.gitignore
README.md		README.md
Snakefile		Snakefile
conda.yaml		conda.yaml
config.yaml		config.yaml
dag.svg		dag.svg
dag_job.svg		dag_job.svg
environment.yaml		environment.yaml
read_group.sh		read_group.sh
singularity.yaml		singularity.yaml
slurm_status.py		slurm_status.py
slurm_wrapper.py		slurm_wrapper.py
variant_count.csv		variant_count.csv