https://github.com/schmytzi/bim_dedup
Deduplicate rsIDs in BIM files for multiallelic SNPs
https://github.com/schmytzi/bim_dedup
Last synced: 3 months ago
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Deduplicate rsIDs in BIM files for multiallelic SNPs
- Host: GitHub
- URL: https://github.com/schmytzi/bim_dedup
- Owner: Schmytzi
- Created: 2019-10-22T11:47:35.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2019-10-22T12:02:43.000Z (over 5 years ago)
- Last Synced: 2025-01-16T04:11:19.771Z (5 months ago)
- Language: Python
- Size: 1.95 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Deduplicate rsIDs in BIM Files
Multiallelic SNPs are encoded as multiple SNPs with the same rsID but different alleles in BIM files used by PLINK.
This can lead to problems with downstream analyses because other tools expect these IDs to be unique.
This script identifies duplicated rsIDs and appends a serial number to make them unique.
## Usage
```
python3 bim_dedup.py [-h] [input]
positional arguments:
input The BIM file to read in. Defaults to STDIN if '-' or no value is
passed
optional arguments:
-h, --help show help message and exit
```
The output is always written to STDOUT.