Connect with us

Software

vcf2fhir- A New Tool to Convert VCF files into HL7 FHIR Format

Published

on

vcf2fhir

A new utility is developed to convert variant calling format (VCF) files into HL7 FHIR format for the purpose of genomics electronic health records (EHR) integration. This is known as vcf2fhir [1].

Fast healthcare interoperability resource (FHIR) is a data format and an application programming interface to exchange EHR. HL7 FHIR language is an emerging language for EHR interoperability. vcf2fhir utility converts VCF files into HL7 FHIR diagnostic report.

How does vcf2fhir work?

  • It takes the VCF file as input.
  • vcf2fhir converts each row in the VCF file into a corresponding FHIR-formatted variant.
  • These variants include MNVs, SNVs, Indels, zygosity, and phase relationship.
  • Users are allowed to input genome build (‘GRCh37’ or ‘GRCh38’), a conversion region, a studied region that includes genomic regions already studied, and a non-callable region that includes studied uncallable regions.

The source code of vcf2fhir is available on Github. The software is written in python and is platform-independent.

For further information, read here.


References

  1. Dolin, R.H., Gothi, S.R., Boxwala, A. et al. (2021). vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. BMC Bioinformatics 22, 104.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Advertisement
Click to comment

You must be logged in to post a comment Login

Leave a Reply

MD Simulation

[Tutorial] Installing VIAMD on Ubuntu (Linux).

Dr. Muniba Faiza

Published

on

[Tutorial] Installing VIAMD on Ubuntu (Linux).

Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows the interactive analysis of molecular dynamics simulations [1]. In this article, we are installing it on Ubuntu (Linux).

(more…)

Continue Reading

Docking

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

Dr. Muniba Faiza

Published

on

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.

(more…)

Continue Reading

Docking

How to install the DockingPie plugin on PyMOL?

Dr. Muniba Faiza

Published

on

How to install DockingPie plugin on PyMOL?

DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).

(more…)

Continue Reading

Software

Video Tutorial: Calculating binding pocket volume using PyVol plugin.

Dr. Muniba Faiza

Published

on

Calculate Binding Pocket Volume in Pymol (using PyVol plugin).

This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].

(more…)

Continue Reading

Software

How to generate topology from SMILES for MD Simulation?

Dr. Muniba Faiza

Published

on

How to generate topology from SMILES for MD Simulation?

If you need to generate the topology of molecules using their SMILES, a simple Python script is available.

(more…)

Continue Reading

Software

[Tutorial] Installing jdock on Ubuntu (Linux).

Dr. Muniba Faiza

Published

on

[Tutorial] Installing jdock on Ubuntu (Linux).

jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).

(more…)

Continue Reading

Software

How to upgrade cmake on Ubuntu (Linux)?

Dr. Muniba Faiza

Published

on

How to upgrade cmake on Ubuntu/Linux?

In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)

Continue Reading

Software

How to install GMXPBSA on Ubuntu (Linux)?

Dr. Muniba Faiza

Published

on

How to install GMXPBSA on Ubuntu (Linux)?

GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).

(more…)

Continue Reading

Docking

[Tutorial] Installing Pyrx on Windows.

Dr. Muniba Faiza

Published

on

[Tutorial] Installing Pyrx on Windows.

Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)

Continue Reading

MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Dr. Muniba Faiza

Published

on

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.

(more…)

Continue Reading

Software

Installing Autodock4 on MacOS.

Dr. Muniba Faiza

Published

on

Installing Autodock4 on MacOS

Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.

(more…)

Continue Reading

Docking

How to install Autodock4 on Ubuntu?

Dr. Muniba Faiza

Published

on

How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.

(more…)

Continue Reading

Software

DS Visualizer: Uses & Applications

Dr. Muniba Faiza

Published

on

DS Visualizer: Uses & Applications

Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.

(more…)

Continue Reading

Software

Protein structure & folding information exploited from remote homologs.

Dr. Muniba Faiza

Published

on

protein structure & folding prediction using remote homologs

Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)

Continue Reading

RNA-seq analysis

Pathonoia- A new tool to detect pathogens in RNA-seq data.

Dr. Muniba Faiza

Published

on

Pathonoia- A new tool to detect pathogens in RNA-seq data.

Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].

(more…)

Continue Reading

Software

AlphaFill- New algorithm to fill ligands in AlphaFold models.

Dr. Muniba Faiza

Published

on

AlphaFill- New algorithm to fill ligands in AlphaFold models.

AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)

Continue Reading

Software

How to calculate binding pocket volume using PyVol plugin in PyMol?

Dr. Muniba Faiza

Published

on

How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

Continue Reading

Software

How to generate electron density map using Pymol?

Dr. Muniba Faiza

Published

on

How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.

(more…)

Continue Reading

Software

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

Dr. Muniba Faiza

Published

on

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)

Continue Reading

Software

How to execute matlab from terminal in Ubuntu (Linux)?

Dr. Muniba Faiza

Published

on

How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.

(more…)

Continue Reading

LATEST ISSUE

ADVERT