https://github.com/wickdchromosome/variant_level_gene_annotation

Quick script that adds a gene column to variant level phaser output based on a gencode annotation file
https://github.com/wickdchromosome/variant_level_gene_annotation

Last synced: 26 days ago
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Quick script that adds a gene column to variant level phaser output based on a gencode annotation file

• Host: GitHub
• URL: https://github.com/wickdchromosome/variant_level_gene_annotation
• Owner: wickdChromosome
• Created: 2020-12-08T02:55:06.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2020-12-10T00:46:04.000Z (almost 4 years ago)
• Last Synced: 2024-03-12T15:29:10.568Z (8 months ago)
• Language: Shell
• Size: 2.73 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# Phaser variant level gene annotation

This is just a quick script that adds gene annotation using the hg38 gencode gene annotation file included in this repo(from https://www.gencodegenes.org/human/). A few notes:

	- Variants overlapping more than one annotation will have multiple lines in the output file 

	- the missing value notation when there's no annotation is "."

	- This script was tested with the current hg38 annotation file from gencode(included in this repo).

Bedtools is a dependency for this script, which can be downloaded from: https://bedtools.readthedocs.io/en/latest/content/installation.html#downloading-a-pre-compiled-binary 

### Example usage

```

bash annotate.sh chr1.allelic_counts.txt GENCODE_gencode.v26.GRCh38.genes.bed out.txt 

```