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