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
- Upload VCF file
- Import VCF file into a project's VCF store
- Define sample-participant mapping table
- Download statistics
- 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