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

serial: '46'
sid: '149885'
uuid: dfc7dd67-0309-4aa7-a00e-108c0952f586
uri: /nci/ccdisymposium/abstract
created: '1756242855'
completed: '1756242982'
changed: '1756242982'
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langcode: en
webform_id: ccdi_symposium_abstract
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entity_id: '2139'
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data:
  authors_:
    - add_author_degree: PhD
      add_author_first_name: Michael
      add_author_last_name: Sierk
      add_author_middle: ''
      add_author_organization: 'National Cancer Institute'
    - add_author_degree: PhD
      add_author_first_name: Justin
      add_author_last_name: Elfritz
      add_author_middle: ''
      add_author_organization: IBM
    - add_author_degree: PhD
      add_author_first_name: Kate
      add_author_last_name: Isaac
      add_author_middle: ''
      add_author_organization: 'Fred Hutch Cancer Center'
    - add_author_degree: BA
      add_author_first_name: Thomas
      add_author_last_name: "O'Neal"
      add_author_middle: ''
      add_author_organization: IBM
    - add_author_degree: PhD
      add_author_first_name: Daoud
      add_author_last_name: Meerzaman
      add_author_middle: ''
      add_author_organization: 'National Cancer Institute'
  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_title_: 'VCF Table Viewer: Flexible Visualization of CCDI VCF Files'
  email_address_: michael.sierk@nih.gov
  institution_: 'National Cancer Institute'
  presenting_author_: 'Michael Sierk'