Using GOR in Notebooks

GOR can be combined with Python, R or SPARK through Jupyter notebooks using our relevant SDKs. This allows the user to efficiently query genomic data while reading desired information into data frames opening the door to the advanced plotting and analysis tools of R or Python.

To create a new notebook select the Notebooks options from the current platform. You will be taken to a jupyter hub server page where you can create a new notebook from scratch or copy one of the built-in template notebooks from the GOR/ folder to your user directory.

Notebook Examples

Below are examples of notebooks showcasing GOR query analysis.

Notebooks with GOR examples

Notebook	Description
AF VEP Join	Joining variant allele frequency information with variant effect prediction information
Extract Variants	Demonstrate the basic commands to extract variants from a genotype freeze
Gnomad	Here we will show how we can take very large VCF files from the Genome Aggregation Database and convert them to GOR tables.
GOR Helper Demo	Demonstration of how to use the GOR helper in notebooks.
GWAS Comparison	Demonstrate functionality to compare different GWAS runs
GWAS vs. Finngen	Comparison of Plink GWAS with Finngen results in Analysis Catalog structure
HPO	Working with the HPO direct acyclic graph (DAG)
HPO Phecode	HPO phenotypes and Phecode-like catalog
HPO Phewas	HPO Phewas based on a Phecode-like catalog
ICD Longitudinal	Longitudinal phenotype analysis
Joins	Genome JOINS
LD	Linkage disequilibrium
Parallel Queries: PARALLEL	Parallel GORpipe queries with PARALLEL
Parallel Queries: PARTGOR	Parallel GORpipe queries with PARTGOR
Parallel Queries: PGOR	Parallel GORpipe queries with PGOR
AF comparison of Gnomad WGS vs WES	AF comparison of Gnomad WGS vs WES
CNV annotations for Gregor - draft	CNV annotations for Gregor - draft
CNV features for variant scoring	CNV features for variant scoring
CNVs from multiple XA-samples analysed	CNVs from multiple XA-samples analysed
Exon coverage analysis	Exon coverage analysis
Genome Browser tracks	Genome Browser tracks
Gene drill-in query	Gene drill-in query
GnomAD variant liftover	GnomAD variant liftover
Gregor1 SNV preprocessing	Gregor1 SNV preprocessing
Gregor2 SNV postprocessing	Gregor2 SNV postprocessing
Excecuting Gregor step1 and step2	Excecuting Gregor step1 and step2
Incremental AF calculation	Incremental AF calculation
Incremental horizontal (pVCF-like) genotype generation	Incremental horizontal (pVCF-like) genotype generation
Liftover of Clinvar	Liftover of Clinvar
SNV variant feature generation for ranking	SNV variant feature generation for ranking
Relationship analysis with King and Queen	Relationship analysis with King and Queen
Run Gregor studies in batch	Run Gregor studies in batch
SMN1 calling from BAM files	SMN1 calling from BAM files
Uniparental disomy (UPD)	Uniparental disomy (UPD)
XA report builder query demo	XA report builder query demo