A Python package for downsampling sequence alignment files.
pydownsampler is available through pypi. To install, type:
pip install pydownsampler$ pydownsampler (<file>) [-d <dcov>]
$ pydownsampler (<file>) [-d <dcov>] [-o <output>]
$ pydownsampler (<file>) [-c]
$ pydownsampler [-h] | [--help]
$ pydownsampler [-v] [--version]| Argument/ Option | Description |
|---|---|
-h, --help |
Show help message to screen. |
-v, --version |
Show version. |
<file> |
Input BAM/CRAM/SAM file |
-d, --downcoverage |
The coverage you want to downsample to (Required argument) |
-o, --output |
Output filename prefix (Optional) |
-c, --coverage |
Check file coverage |
# option 1 (default):
$ pydownsampler input.bam -d 10
In the example above, the file 'input.bam' will be downsampled to 10X coverage. The output filename will be 'input.Downsampled10X.bam'.
# option 2 (optional):
$ pydownsampler input.bam -d 10 -o downsampled
# check coverage of a BAM/CRAM/SAM file
$ pydownsampler input.bam -cpydownsampler is generously distributed under The MIT License