monkiky/calculate-coverage repository overview

This python scripts utilize bam file using samtools to calculate coverage percentage by gene, exon, and panel. In addition, it generates a list of coverage gaps.

⁠Getting Started

⁠Installing

virtualenv

git clone [email protected]:cas-wrgl/calculate-coverage.git
cd calculate-coverage
python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

docker

docker build -t calculate-coverage:latest .

apptainer

apptainer build apptainer.sif apptainer.def

⁠Executing program

Input:

• Aligned data, prepared as bam file
• BED file with no overlaping intervals of the same gene. The name field should be in the format: gene_transcript_exon

Output (text format):

• (i) coverage % by gene
• (ii) coverage % by exon
• (iii) a list of coverage gaps

python main.py \
--bam_file BAM_FILE \
--bed_file BED_FILE \
--sample_id SAMPLE \
[--MQ MQ] \
[--overlapping_section OVERLAPPING_SECTION] \
[--min_DP MINIMUM_DEPTHOFCOVERAGE] \

⁠Unit tests

• How to run the unit tests

python -m pytest -v tests