BWA pipeline - Genomics pipeline based on BWA (Burrows Wheeler Alignment)

Description

Edit bwa_config.json for the paths to your data, results and tools. Then execute

./bwa_pipeline.py <directory in data_dir>

Name		Name	Last commit message	Last commit date
Latest commit History 33 Commits
images		images
.gitignore		.gitignore
Dockerfile		Dockerfile
README.md		README.md
bcftools.py		bcftools.py
bwa_config.json		bwa_config.json
bwa_pipeline.py		bwa_pipeline.py
gatk.py		gatk.py
get_sra_url.py		get_sra_url.py
make_bwa_job.py		make_bwa_job.py
run.sh		run.sh
run_bwa.sh		run_bwa.sh
samtools.py		samtools.py
snpeff.py		snpeff.py
varscan.py		varscan.py
vcfutil.py		vcfutil.py