Script to parse annotated vcf files (VEP,snpEff,ANNOVAR) to a csv table
- -v, --vcf [Path of the annotated VCF file to parse]
- -o, --output [Path of the output CSV table]
Split snpEff/VEP transcripts by rows and internal pipe separator by columns
- -t, --splitAnnotator ['s' for snpeff, 'v' for vep, 's,v' for both snpeff and vep together]
Example:
python3 AnnotatedvcfParser.py -v path/to/AnnotatedVcf.vcf -o path/to/Example.csv
python3 AnnotatedvcfParser.py -v path/to/VepVcf.vcf -o path/to/Example.csv --splitAnnotator v
python3 AnnotatedvcfParser.py -v path/to/snpEffVcf.vcf -o path/to/Example.csv --splitAnnotator s
You can find all the information inside the jupyter notebook inside this repository. (see:AnnotatedvcfParser.ipynb)
License MIT