deepCSA

deepCSA Test Datasets

This folder contains test data to be used for automated testing with the bbglab/deepCSA pipeline (https://github.com/bbglab/deepCSA).

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Content of this repository

deepCSA/testdata/maf/ : Somatic mutation calls (MAF format) for all samples. deepCSA/testdata/depth/ : Per-sample sequencing depth table.

Full tree:

.
└── deepCSA
    └── testdata
        ├── depth
        │   └── all_samples_indv.depths.tsv.gz
        └── maf
            └── all_samples.somatic.mutations.maf

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Dataset information

This is a small subset (3 samples) of the normal bladder urothelium dataset published in:

Calvet, F., Blanco Martinez-Illescas, R. et al.
"Sex and smoking bias in the selection of somatic mutations in human bladder."
Nature (2025). https://doi.org/10.1038/s41586-025-09521-x

The full dataset is publicly available at Zenodo:

https://zenodo.org/records/15836679
DOI: 10.5281/zenodo.15836679

Samples included

Sample ID	Description
P19_0002_BDO_01	Normal bladder urothelium
P19_0002_BTR_01	Normal bladder urothelium
P19_0003_BDO_01	Normal bladder urothelium

How to obtain the test files from Zenodo

Download and extract the Zenodo archive:

wget https://zenodo.org/records/15836679/files/normal_bladder_urothelium.tar.gz
tar -xzf normal_bladder_urothelium.tar.gz

The three samples in this test dataset are a subset of the full cohort.

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Reference files

Running deepCSA requires several external reference files. These are NOT included in this repository due to size constraints. Below is a list of the required files and where to obtain them, following the documentation at:

https://github.com/bbglab/deepCSA/blob/main/docs/usage.md

Usage in the pipeline (test configuration)

The test uses pre-computed mutation calls and depth tables instead of running from raw BAM/VCF files. The relevant test parameters are:

input_maf             = "path/to/deepCSA/testdata/maf/all_samples.somatic.mutations.maf"
use_custom_depths     = true
custom_depths_table   = "path/to/deepCSA/testdata/depth/all_samples_indv.depths.tsv.gz"
use_custom_minimum_depth = 10

See the pipeline test suite documentation for more details:

https://github.com/bbglab/deepCSA/blob/main/tests/README.md
https://github.com/bbglab/deepCSA/pull/438