Checks whether header has a CSQ tag
Checks whether header has a CSQ tag
VCF header
Explode a single VEP-annotated record to multiple normal records Based on the number of annotated transcripts in the CSQ tag
Explode a single VEP-annotated record to multiple normal records Based on the number of annotated transcripts in the CSQ tag
the record as a VariantContext object
An array with names of new info tags
An array with the new records
Normalizer
Normalizer
input VCF VCFFileReader
output VCF AsyncVariantContextWriter
array of string containing names of new info fields
normalizer mode (explode or standard)
remove csq tag (Boolean)
Parses the CSQ tag in the header
Parses the CSQ tag in the header
the VCF header
list of strings with new info fields
Checks whether version of input VCF is at least 4.0 VEP is known to cause issues below 4.0 Throws exception if not
Checks whether version of input VCF is at least 4.0 VEP is known to cause issues below 4.0 Throws exception if not
VCFHeader of input VCF