get_variant_allele_fraction: Get the variant allele fraction from the FORMAT string.

In Bio-Core/BioCore.Annotation: BioCore Variant Annotation Package

Description

A method to parse the FORMAT string and extract the variant allele fraction (FA field).

Usage

get_variant_allele_fraction(data=NULL, delimiter=':', vaf_index=15)

Arguments

data	an ANNOVAR dataframe (required)
delimiter	field delimiter used in the FORMAT string (default: :)
vaf_index	index within the FORMAT string for the variant allele fraction (default: 15)

Value

Returns the variant allele fraction for the given variant.

Author(s)

Richard J. de Borja

Examples

  format_string = '1/1:41:8:8:0:8:100:7.77E-5:0:50:0:0:6:2:1.0000'
  print(get_variant_allele_fraction(data=format_string))

Bio-Core/BioCore.Annotation documentation built on Feb. 3, 2020, 6:01 p.m.