Childhood Cancer Data Initiative Annual Symposium (Abstract Registration): Submission #46

Abstract Submission for Poster Presentation
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Abstract Title:: VCF Table Viewer: Flexible Visualization of CCDI VCF Files
Abstract::
Variant calling pipelines produce variant caller format (VCF) files.  VCF files have large amounts of information about called variants, especially if they are annotated by tools such as Variant Effect Predictor (VEP), but are difficult to read and interpret directly, particularly for non-computational biologists.  Thus, there are many tools available to extract information from VCF files for visualization and analysis.  We present here a new Shiny app, VCF Table Viewer, that extracts information from annotated VCF files and displays them in an interactive table.  The table provides the ability to flexibly sort through a list of called variants while visualizing desired annotations, including color highlighting of various annotations.  It also allows easy visualization of the bam file pileups in an embedded IGV tab for variants selected in the table, as well as plots of somatic allele frequencies from mutect2 calls over multiple samples when these are available.  VCF Table Viewer provides a novel interface that facilitates the examination of variant calls by non-computational biologists. We provide examples from an ongoing clinical study of patients with familial platelet disorder.  The code is freely available on Github and has been integrated into the Cancer Genomics Cloud with easy selection of VCF files from CCDI datasets for visualization.

Abstract:: {Empty}
Authors::
1. First Name: Michael
   Last Name: Sierk
   Degree(s): PhD
   Organization: National Cancer Institute
2. First Name: Justin
   Last Name: Elfritz
   Degree(s): PhD
   Organization: IBM
3. First Name: Kate
   Last Name: Isaac
   Degree(s): PhD
   Organization: Fred Hutch Cancer Center
4. First Name: Thomas
   Last Name: O'Neal
   Degree(s): BA
   Organization: IBM
5. First Name: Daoud
   Last Name: Meerzaman
   Degree(s): PhD
   Organization: National Cancer Institute

Presenting Author:: Michael Sierk
Institution:: National Cancer Institute
Email Address:: michael.sierk@nih.gov