https://github.com/dfornika/aa-table-with-af
Convert a .vcf file to 'aa_table.tsv', including depth & alt frequency info
https://github.com/dfornika/aa-table-with-af
Last synced: 3 months ago
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Convert a .vcf file to 'aa_table.tsv', including depth & alt frequency info
- Host: GitHub
- URL: https://github.com/dfornika/aa-table-with-af
- Owner: dfornika
- Created: 2021-10-15T19:06:04.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2021-10-15T20:59:42.000Z (over 3 years ago)
- Last Synced: 2025-01-24T23:49:12.660Z (4 months ago)
- Language: Python
- Size: 3.91 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# aa-table-with-af
Produce an 'amino acid table' file from a vcf, including depth and alt frequency info.
## Dependencies
This script uses [`pysam`](https://github.com/pysam-developers/pysam) to parse `.vcf` files.
pysam is available on both [pypi](https://pypi.org/project/pysam/) and [bioconda](https://anaconda.org/bioconda/pysam).
## Usage
```
usage: aa_table_with_af.py [-h] [-s SAMPLE_ID] vcf
positional arguments:
vcf
optional arguments:
-h, --help show this help message and exit
-s SAMPLE_ID, --sample_id SAMPLE_ID
```