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Welcome to the BAM_QC wiki!
This tool is meant to compute a few basic metrics over alignment files (BAM or CRAM format). Mean Insert size, percentage of unmapped or OFF-Target reads are computed for each sample. The relatedness for sample couple is also tested. Sample information are then summarized in TSV tables.
To run this workflow, conda is required and mamba is strongly recommended. Please note that it has been developed on a linux operating system.
To create the environment to run the workflow, just run the following command:
mamba create -n snake_env -c bioconda -c conda-forge snakemake numpy matplotlib
Activate this environment via the command:
conda activate snake_env
A test of the workflow can be performed by running the script .test/get_files.sh to downlaod required files. Note that the reference genome and the sites file from the .test/data_test directory can be used for your own analysis.
Once files have been downloaded, you can run the test through the command snakemake -s workflow/Snakefile.smk -j 5 --use-conda --configfile .test/config.yaml
All settings can be modified from the config/config.yaml file. The table underneath describes them.
| parameter | description | default |
|---|---|---|
| CRAM_list | List of input files (use absolute paths). 1 per line. | None (Required) |
| reference | A reference file in FASTA format (can be bgzipped). | None (Required) |
| samples_list | List of samples to be processed, 1 per line (Should match the sample names indicated in the alignment files). | None (Required) |
| regions | Target regions in bed format | None (Required) |
| sites_som | Sites to be used to compute relatedness, in VCF format (see https://github.com/brentp/somalier/releases). | None (Required) |
| prefix | Prefix to use for output files. | 'alignmentQC' |
| outdir | Path to output directory. | '.' |
| tempdir | Path to working directory. An alternative is to use the snakemake --workdir option. |
'.' |
The workflow can be launched using the command snakemake -s workflow/Snakefile.smk -j <n_threads> --use-conda. Default configuration file will be config/config.yaml.