Quickstart

Eager to get started? This page gives a good introduction in how to get started with vcf2fhir.

Installation

Installing vcf2fhir is pretty simple. Here is a step by step plan on how to do it.

Note

vcf2fhir is available on Pypi as vcf2fhir.

Before installing vcf2fhir you need to install cython and wheel:

pip install cython wheel
pip install vcf2fhir

This will install vcf2fhir library.

Examples

(some sample VCF files are here)

Quick example

import vcf2fhir
vcf_fhir_converter = vcf2fhir.Converter('sample.vcf', 'GRCh37')
vcf_fhir_converter.convert()

More Example to instantiate Converter

  • Converts all variants in VCF. FHIR report contains no region-studied observation.
vcf2fhir.Converter('vcftests.vcf','GRCh37', 'aabc')

  • Converts all variants in VCF. FHIR report assign homoplasmic vs. heteroplasmic based on:

    If allelic depth (FORMAT.AD)/ read depth (FORMAT.DP) is greater than 0.89 then allelic state is homoplasmic; else heteroplasmic.

    Note : default value of ratio_ad_dp = 0.99 and ratio_ad_dp is considered valid only when value lies between 0 and 1

    vcf2fhir.Converter('vcftests.vcf','GRCh37', 'aabc', ratio_ad_dp = 0.89)

  • Submitting only noncallable region without other regions generates an error.

vcf2fhir.Converter('vcftests.vcf','GRCh37', 'babc', nocall_filename='WGS_b37_region_noncallable.bed')
  • Converts all variants in VCF. FHIR report contains one region-studied observation per studied chromosome.
vcf2fhir.Converter('vcftests.vcf','GRCh37', 'cabc', region_studied_filename='WGS_b37_region_studied.bed')
  • Converts all variants in VCF. FHIR report contains one region-studied observation per studied chromosome.
vcf2fhir.Converter('vcftests.vcf','GRCh37', 'dabc', region_studied_filename='WGS_b37_region_studied.bed', nocall_filename='WGS_b37_region_noncallable.bed')
  • Converts all variants in conversion region. FHIR report contains no region-studied observation.
vcf2fhir.Converter('vcftests.vcf','GRCh37', 'eabc', conv_region_filename='WGS_b37_convert_everything.bed')
  • Submitting only noncallable region without other regions generates an error.
vcf2fhir.Converter('vcftests.vcf','GRCh37', 'fabc', conv_region_filename='WGS_b37_convert_everything.bed', nocall_filename='WGS_b37_region_noncallable.bed')
  • Converts all variants in conversion region. FHIR report contains one region-studied observation per studied chromosome, intersected with conversion region.
vcf2fhir.Converter('vcftests.vcf','GRCh37', 'gabc', conv_region_filename='WGS_b37_convert_everything.bed', region_studied_filename='WGS_b37_region_studied.bed')
  • Converts all variants in conversion region. FHIR report contains one region-studied observation per studied chromosome, intersected with conversion region.
vcf2fhir.Converter('vcftests.vcf','GRCh37', 'habc', conv_region_filename='WGS_b37_convert_everything.bed', region_studied_filename='WGS_b37_region_studied.bed', nocall_filename='WGS_b37_region_noncallable.bed')
  • Conversion of a bgzipped VCF
vcf2fhir.Converter('vcf_example4.vcf.gz','GRCh37', 'kabc', has_tabix=True)

Logging

You can use python standard logging to enable logs. Two logger (‘vcf2fhir.general’) and (‘vcf2fhir.invalidrecord’) are avialble to configure.

  • vcf2fhir.general: standard library logs.
  • vcf2fhir.invalidrecord: logs all the records from vcf file which are in conversion region but are not converted to fhir format.
>>> import logging
# create logger
>>> logger = logging.getLogger('vcf2fhir.invalidrecord')
>>> logger.setLevel(logging.DEBUG)
# create console handler and set level to debug
>>> ch = logging.FileHandler('invalidrecord.log')
>> ch.setLevel(logging.DEBUG)
# create formatter
>>> formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# add formatter to ch
>>> ch.setFormatter(formatter)
# add ch to logger
>>> logger.addHandler(ch)