Features

• User “Filter VCF” form providing well documented filter options (includes examples) and a variety of formats.

  • Basic filter options include: Only bi-allelic SNPs, Minimum SNP Call Read Depth, Minor Allele Frequency, Maximum Missing Count, Maximum Missing Frequency.
  • More filter options include: regions and germplasm.
  • Export Formats include: VCF, Quality Matrix (read depth only), A/B Biparental Matrix, Hapmap, Bgzipped VCF.

• All filtering and format conversion is done within a Tripal Job to support large files.

• Administrative interface for exposing VCF files to users. Extensive configuration options allow comprehensive description of each VCF file, which can offer great user experience.

  • In addition to specifying the path to the VCF file to expose, record helpful information like a friendly name, assembly aligned to, number of SNPs.
  • The information of the methods used in generating each VCF file, a statistic summary and more description can be included.
  • All germplasm names and Chromosome name format can be included as more helpful information.

• Per VCF file permissions allowing you to restrict access to a given file to specific users or roles.

Further Detail:

• Various Filter Options
  • Restrict dataset to specific germplasm or regions
  • Basic Filtering Options
• Configuration Options
• Restrict Access by Permissions