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Script to parse annotated vcf files (VEP,snpEff,ANNOVAR) to a csv table

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YussAb/AnnotatedvcfParser

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AnnotatedvcfParser.py

Script to parse annotated vcf files (VEP,snpEff,ANNOVAR) to a csv table

Documentation for usage from bash terminal

Options:

Required:

  • -v, --vcf [Path of the annotated VCF file to parse]
  • -o, --output [Path of the output CSV table]

Optional:

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 

Documentation for interactive development environment:

You can find all the information inside the jupyter notebook inside this repository. (see:AnnotatedvcfParser.ipynb)

License MIT

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Script to parse annotated vcf files (VEP,snpEff,ANNOVAR) to a csv table

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