This package has a set of modules to get coverage statistics for targeted DNA sequencing.

Main modules:

• stats-coverage:

coverage.py --run stats-coverage --out out_dir --region region_file.bed *bam

This will generate two files per sample in the out_dir folder: *_cov.csv will have the summary data and *dat the raw coverage information

• bias-coverage:

coverage.py --run bias-coverage --region ../regions.bed --out bias ../sample1.bam --n_sample 20 --seed 42

this will generate the coverage bias information inside the bias folder. Each sample will have *_bias.tsv file.

• cg-vcf:

coverage.py --run cg-vcf --region ../regions.bed --out cg ../sample1.vcf.gz --reference REFERENCE.FA

this will generate *cg-depth-parse.tsv for each sample inside cg folder.

if you already have a bcbio installation working:

git clone https://github.com/lpantano/exomeCov.git git clone https://github.com/lpantano/ich-wrapper.git

export PYTHONPATH=$PATH_to_exomeCov:$PATH_to_ich-wrapper

make sure to use the bcbio python:

python /$PATH_to_exomeCov/scripts/coverage.py

You can do an exec and add it to your path modifying the file scripts/coverage