Metadata-Version: 2.4
Name: rnaseqmut-py
Version: 0.1.0
Summary: Python-only mutation caller workflow for RNA-Seq BAM files
Author: Wei Li
License: MIT
Project-URL: Homepage, https://github.com/davidliwei/rnaseqmut-py
Project-URL: Repository, https://github.com/davidliwei/rnaseqmut-py
Keywords: rna-seq,variant-calling,bam,bioinformatics
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: pysam>=0.23

# rnaseqmut-py

Python-only port of the `rnaseqmut` mutation calling workflow.

- No C++ compiler needed
- Input: sorted/indexed BAM (`.bam` + `.bai`)
- Output: tab-delimited calls on STDOUT and VCF file

## Install

```bash
pip install rnaseqmut-py
```

## Usage

```bash
rnaseqmut sample.bam > sample.txt
```

```bash
rnaseqmut -l mutation_list.txt sample.bam > sample.2nd.txt
```
