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SACGF

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variantgrid
VariantGrid public repo

Python · 30 stars

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Claire Seurat / combined caller data VCFs Open

VCF

SACGF/variantgrid#312 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Merge/Join nodes together as optimisation Open

Analysis

SACGF/variantgrid#313 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Trio recessive filter change Open

SACGF/variantgrid#321 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Multi VCF analysis Open

Analysis

SACGF/variantgrid#322 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Write admin read the docs Open

documentation

SACGF/variantgrid#323 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Sequencing Run - index metrics graph - only show samples in SampleSheet.csv Open

SACGF/variantgrid#326 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
SampleNode flash yellow for coverage like GeneListNode Open

Analysis

SACGF/variantgrid#347 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Analysis node profiling / performance monitoring Open

Analysis

SACGF/variantgrid#351 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
UserSettings Default Sort Column - cascade of default sort, can only have 1 Open

SACGF/variantgrid#358 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
VUS(a/b/c) - clinical significance calculation changes Open

ACMG classification

SACGF/variantgrid#359 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Cloning AnalysisNodes should keep parent connections Open

Analysis

SACGF/variantgrid#362 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Zygosity count - calculate and choose different options Open

SACGF/variantgrid#365 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Variant Tag imports v2 Open

Tagging

SACGF/variantgrid#374 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Gene Symbols matching to many genes - how lax should symbol aliasing be? Open

Gene

SACGF/variantgrid#375 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Analysis - be able to expire client side cache Open

SACGF/variantgrid#382 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
ClassificationNode - enhancements - ClinVar and labs Open

Analysis

SACGF/variantgrid#389 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Minor issues Open

SACGF/variantgrid#392 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
SomalierVCFTask - somalier_all_samples Open

Relatedness

SACGF/variantgrid#393 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Duplicate Allele causes VariantAllele integrity error upon merging Open

bug

SACGF/variantgrid#400 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Large cohort creation jobs Open

SACGF/variantgrid#404 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Gene based analysis Open

Analysis

SACGF/variantgrid#406 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Annotation page - toggle shouldn't show an error Open

documentation

SACGF/variantgrid#414 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Sequencing data / QC - show where files came from Open

SACGF/variantgrid#420 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Patient upload error Open

Patients

SACGF/variantgrid#422 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Ontology Related data v2 Open

Ontology

SACGF/variantgrid#426 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Search - HGVS locus Open

HGVS search

SACGF/variantgrid#437 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Gene / Disease prioritisation Open

SACGF/variantgrid#442 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Multi-variant Classification + Reporting Open

SACGF/variantgrid#444 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
LOH - Loss Of Heterozygosity Open

SACGF/variantgrid#445 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
RNAseq - multi-omics etc Open

SACGF/variantgrid#446 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Performance monitoring Open

optimisation

SACGF/variantgrid#447 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
HGVS Search that also includes gene symbol Open

HGVS search

SACGF/variantgrid#452 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Use 64bit PKs for big tables Open

SACGF/variantgrid#457 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
populate_clingen_alleles_for_variants doesn't handle case where Allele exists, but does not have ClinGen Allele Open

SACGF/variantgrid#490 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
SettingsInitialGroupPermission for lab/organisation Open

SACGF/variantgrid#495 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Dealing with pseudoautosomal (PAR) regions Open

SACGF/variantgrid#506 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
MAF filter - allow filtering by cohorts as well Open

Analysis

SACGF/variantgrid#508 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Flag when ClinGen allele registry used to generate chgvs Open

SACGF/variantgrid#510 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Classification - where reference base doesn't match our reference fasta Open

Reference base

SACGF/variantgrid#517 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Flag Alleles in pseudoautosomal (PAR) regions Open

SACGF/variantgrid#518 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
GeneVersion handle multiple loci Open

SACGF/variantgrid#520 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Fetch PMIDs async after classification import Open

optimisation

SACGF/variantgrid#523 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
ImportTaskFactory - set success/fail on objects Open

SACGF/variantgrid#537 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Autopopulate Mode Of Inheritance Open

classification

SACGF/variantgrid#554 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Analysis - sample tab auto analysis / MOI node tidy up Open

Analysis

SACGF/variantgrid#558 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Github actions - run tests Open

SACGF/variantgrid#565 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
gnomAD AF filters - when people use sub populations Open

Analysis optimisation

SACGF/variantgrid#595 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Investigate using nosql for some faster queries Open

Database enhancement

SACGF/variantgrid#604 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Cache node counts using SQL as key Open

Analysis optimisation

SACGF/variantgrid#607 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Investigate Metadome Open

Annotation

SACGF/variantgrid#634 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026

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