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https://github.com/AndersenLab/bam-toolbox
A bam toolbox
https://github.com/AndersenLab/bam-toolbox
Last synced: 3 months ago
JSON representation
A bam toolbox
- Host: GitHub
- URL: https://github.com/AndersenLab/bam-toolbox
- Owner: AndersenLab
- License: mit
- Created: 2015-10-28T16:36:51.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2024-07-30T17:47:33.000Z (3 months ago)
- Last Synced: 2024-07-31T02:36:02.874Z (3 months ago)
- Language: Python
- Size: 1.77 MB
- Stars: 1
- Watchers: 10
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- Awesome-Bioinformatics - bam toolbox
README
# bam-toolbox
## Installation
```
pip install https://github.com/AndersenLab/bam-toolbox/archive/1.0.0.tar.gz
```
## Usage
bam-toolbox 1.0
usage:
bam [...]
bam -h | --help
bam --version
commands:
coverage
## Commands
### Coverage
Calculate depth of coverage! There are several ways to do so:
1. Calculate coverage for the whole genome, nuclear genome, and individual chromosomes. Also calculated the mtDNA:nuclear ratio which acts as a proxy for mitochondrial content.
2.
```
usage:
bam coverage [options] [--mtchr=]
bam coverage [options] ...
bam coverage [options] --window=
bam coverage [options] --regions=
```
###### Parameters
* `--header` - Output the header line.
* `--mtchr` - Specifying a mitochondrial chromosome will output the mtDNA:nuclear DNA ratio, offering an estimate of mitochondrial content.
* `--window` - Calculate depth of coverage for given windows across the genome.
* `--regions` - Specify a bed or gff file and calculate coverage in those regions.
###### Example
```
bam coverage test.bam --tsv --header
```
__Result:__
Output is in `--tsv` format.
```
ENTITY chrom start end ATTR VALUE DATE
CB4853 I 1 15072434 bases_mapped 1688210 2015-11-08 23:22:39.498133
CB4853 I 1 15072434 depth_of_coverage 0.112006461597 2015-11-08 23:22:39.498242
CB4853 I 1 15072434 breadth_of_coverage 0.0918075342045 2015-11-08 23:22:39.498328
CB4853 I 1 15072434 length 15072434 2015-11-08 23:22:39.498372
CB4853 I 1 15072434 pos_mapped 1383763 2015-11-08 23:22:39.498413
CB4853 II 1 15279421 bases_mapped 1605336 2015-11-08 23:22:39.923802
CB4853 II 1 15279421 depth_of_coverage 0.105065237747 2015-11-08 23:22:39.923880
...
CB4853 mt_nuclear_ratio 51.7503772943 2015-11-08 23:22:41.949819
```
__Formatted Result:__
| ENTITY | chrom | start | end | ATTR | VALUE | DATE |
|:---------|:--------|--------:|---------:|:--------------------|------------:|:---------------------------|
| CB4853 | I | 1 | 15072434 | bases_mapped | 1.68821e+06 | 2015-11-08 23:26:41.891988 |
| CB4853 | I | 1 | 15072434 | depth_of_coverage | 0.112006 | 2015-11-08 23:26:41.892087 |
| CB4853 | I | 1 | 15072434 | breadth_of_coverage | 0.0918075 | 2015-11-08 23:26:41.892155 |
| CB4853 | I | 1 | 15072434 | length | 1.50724e+07 | 2015-11-08 23:26:41.892198 |
| CB4853 | I | 1 | 15072434 | pos_mapped | 1.38376e+06 | 2015-11-08 23:26:41.892239 |
| CB4853 | II | 1 | 15279421 | bases_mapped | 1.60534e+06 | 2015-11-08 23:26:42.319937 |