API

vcf2fhir.Converter

class vcf2fhir.Converter(vcf_filename=None, ref_build=None, patient_id=None, has_tabix=False, conv_region_filename=None, conv_region_dict=None, region_studied_filename=None, nocall_filename=None, ratio_ad_dp=0.99)

Creates a new Converter Object to convert a VCF file.

vcf_filename (required): Path to a text-based or bgzipped VCF file. Valid path and filename without whitespace must be provided. VCF file must conform to VCF Version 4.1 or later. FORMAT.GT must be present. Multi-sample VCFs are allowed, but only the first sample will be converted. has_tabix (required if VCF file is bgzipped): Set to ‘True’ if there is a tabix index. Tabix file must have the same name as the bgzipped VCF file, with a ‘.tbi’ extension, and must be in the same folder.

ref_build (required): Genome Reference Consortium genome assembly to which variants in the VCF were called. Must be one of ‘GRCh37’ or ‘GRCh38’.

patient_id (optional): Supplied patient ID is inserted into generated FHIR output. Alphanumeric string without whitespace. if not provided, header of first sample column is used.

Conversion region (optional): Subset of the VCF file to be converted into FHIR. If absent, the entire VCF file is converted. Can be supplied as either a parameter (conv_region_dict) or as a BED file (conv_region_filename):

conv_region_dict : Array of regions (e.g. ‘{“Chromosome”: [“X”, “X”, “M”],”Start”: [50000, 55000, 50000],”End”: [52000, 60600, 60025]}’). Values for Chromosome must align with values in VCF #CHROM field. Ranges must be 0-based (or 0-start, half-open) and based on GRCh37 or GRCh38 reference sequences.

conv_region_filename: Valid path and filename without whitespace must be provided. Must be a valid BED file with first 3 columns: <chr> <start> <stop>. Values in <chr> field must align with values in VCF #CHROM field. Ranges must be based on GRCh37 or GRCh38 reference sequences. Note that BED files are 0-based (or 0-start, half-open) whereas VCF files and FHIR output are 1-based (or 1-start, fully-closed).

region_studied_filename (optional): Subset of patient’s genome that was studied in the generation of the VCF file. Valid path and filename without whitespace must be provided. Must be a valid BED file, with first 3 columns: <chr> <start> <stop>. Values in <chr> field must align with values in VCF #CHROM field. Ranges must be based on GRCh37 or GRCh38 reference sequences. Note that BED files are 0-based (or 0-start, half-open) whereas VCF files and FHIR output are 1-based (or 1-start, fully-closed).

nocall_filename (optional): Subset of studied region that is deemed noncallable. Valid path and filename without whitespace must be provided. Must be a valid BED file, with first 3 columns: <chr> <start> <stop>. Values in <chr> field must align with values in VCF #CHROM field. Ranges must be based on GRCh37 or GRCh38 reference sequences. Note that BED files are 0-based (or 0-start, half-open) whereas VCF files and FHIR output are 1-based (or 1-start, fully-closed).

ratio_ad_dp (optional)(default value = 0.99): This ratio determine whether to assign Homoplasmic or Heteroplasmic

If allelic depth (FORMAT.AD) / read depth (FORMAT.DP) is greater than ratio_ad_dp then allelic state is

homoplasmic; else heteroplasmic.

Object An Instance of Converter that helps to convert vcf file.

convert(output_filename='fhir.json')

Generates HL7 FHIR Genomics format data as output_filename or fhir.json if it is not provided

output_filename:

Path to output fhir json.