Details
-
Type: Improvement
-
Status: Closed (View Workflow)
-
Priority: Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 9.0.2 Minor Release
-
Labels:
-
Story Points:2
-
Sprint:Fall 2018 1, Fall 2018 Sprint 2
Description
Support newer VCF formats in IGB.
(User request)
Attachments
Issue Links
- relates to
-
HELP-303 VCFv4 compatibility
- Closed
I think this is the file I will need to change, possibly the only file.
core/genometry/src/main/java/com/affymetrix/genometry/symloader/VCF.java
This post is helpful:
https://bioinformatics.stackexchange.com/questions/344/whats-the-difference-between-vcf-spec-versions-4-1-and-4-2
For reference, the PDF Samtools specification for VCF 4.1 (currently supported in IGB), 4.2 (not yet supported), and 4.3 (not yet supported)
https://samtools.github.io/hts-specs/VCFv4.1.pdf
https://samtools.github.io/hts-specs/VCFv4.2.pdf
https://samtools.github.io/hts-specs/VCFv4.3.pdf