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https://github.com/baderlab/sc_variant_profiler
A variant calling pipeline for single-cell RNAseq data
https://github.com/baderlab/sc_variant_profiler
Last synced: about 5 hours ago
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A variant calling pipeline for single-cell RNAseq data
- Host: GitHub
- URL: https://github.com/baderlab/sc_variant_profiler
- Owner: BaderLab
- License: mit
- Created: 2021-03-01T21:42:17.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2021-03-01T21:53:36.000Z (almost 4 years ago)
- Last Synced: 2024-11-05T10:26:04.145Z (about 2 months ago)
- Language: Python
- Size: 15.6 KB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## sc_variant_profiler
A variant calling pipeline for single-cell RNAseq data
to split your main BAM file to single cell BAM files use:
```bash
python split_bam_to_cells.py
```
to use the pipeline in python environment run:
```bash
python main.py -h
```
### in order to run the pipeline in scinet hpc check out the bash files:
```bash
Variant_calling_bash_script.sh
batch_Script_for_scinet.sh
```