VCF_Annotation

Introduction

The VCF annotation tool is used to make additional annotations from basic VCF.

How to use it

This tool use only basic module on Python3.(requests, sys, re, json)

Run commend

./anno.py [input_vcf] [output_vcf]
ex) python anno.py clean_challenge.vcf clean_challenge_anno.vcf

###Aditional Annotation columns

1. Type: variant types, such as substitution, deletion, duplication, insertion, inversion, deletion-insertion, complex, other
2. Depth: Depth of sequence coverage at the site of variation
3. Percentage_ALT: Percentage of reads supporting the variant
4. Gene_ID: Use the variant gene_id annotation from ensembl (Ensembl Release 105)https://rest.ensembl.org/?content-type=text/html It separate by comma for multiplue gene_ids.
5. Transcript_ID: Use the variant transcript_id annotation service from ensembl (Ensembl Release 105)https://rest.ensembl.org/?content-type=text/html It separate by comma for multiplue transcript_ids.