KipoiVCFParser

KipoiVCFParser(self, vcf_file)

Iteratively parse a vcf file into a dictionary. This class was designed to work well with VCFs annotated by kipoi-veff. It performs automated shortening of column names.

Arguments

• vcf_file: .vcf file path (can be also .vcf.gz, .bcf, .bcf.gz)

Notes

Iterator returns a nested dictionary with the schema:

 - variant:
   - id
   - chr
   - pos
   - ref
   - alt
 - other:
   - f1
   - f2
 - kipoi:
   - model:
     - type:
       - feature1...
       - feature2...