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

Releases

• Opal 2.9
• Jennite VCF Store 1.0