Opal 2.9

Genotypes

Objectives

  • Storing genotypes data within a project
  • Providing basic statistics on the genotypes
  • Extracting genotypes according to phenotype criteria

New features

  • Genotypes are stored in Variant Call Format (VCF) files
  • VCF store service is a plugin
  • VCF sample - participant association
  • Import of VCF files
  • Export of VCF files, optionally subset by participants

Requirements

  • VCF Store service uses Samtools applications
    • bcftools (statistics and extractions)
    • tabix (indexing)
    • bgzip (compression)
  • VCF files must be sorted, compression is optional

Flow

  1. Upload VCF file
  2. Import VCF file into a project's VCF store
  3. Define sample-participant mapping table
  4. Download statistics
  5. Export VCF file, subset by participants

Sample-Participant Mapping

A table about Samples that defines

  • associated participant ID, a participant can be associated to several samples
  • sample role, sample or control

Sample-Participant Mapping

ID ParticipantID Role
sample1 1111 sample
sample2 2222 sample
sample3 2222 sample
sample4 sample
sample5 control

Releases

  • Opal 2.9
  • Jennite VCF Store 1.0

Opal 2.9

By Yannick Marcon

Opal 2.9

Genotypes, VCF/BCF file store, association with phenotypes

  • 963
Loading comments...

More from Yannick Marcon