10:30-1:50:00 - Oscar Florez-Vargas

(TCGA, ICGC, GTEx)

• https://observablehq.com/@episphere/gtex

• https://observablehq.com/@episphere/tcga

• https://observablehq.com/@episphere/icgc

• https://observablehq.com/@episphere/firebrowse

• 
  

10:50-11:00 - Tom Ahearn

Reading compressed files (FAIRly ...) from remote repositories.

Reference libraries:

• https://episphere.github.io/vcf

• https://episphere.github.io/pgs

target url:

11:00-11:30 - Charles Breeze

Continuation of last week study of operating polygenic risk scores at PGS Catalog.

• https://observablehq.com/@episphere/icgc

[3/12 12:11 AM] Breeze, Charles (NIH/NCI) [F]
A solution to get positions for hg38 from rsids is:
UCSC table browser https://genome.ucsc.edu/cgi-bin/hgTables

Options:

assembly=hg38, group=variation,
identifiers-> paste list of rsids, press submit,

output format=selected fields, press “get output”,

select (√) chrom+chromEnd+name, press “get output”.

​

There might be an API too

--- Notes ---

PLCO GWAS is indexed to hg38

Breeze, Charles (NIH/NCI) [F] to Everyone

dbSNP Reference SNP (rs or RefSNP) number is a locus accession for a variant type assigned by dbSNP. The RefSNP catalog is a non-redundant collection of submitted variants which were clustered, integrated and annotated. RefSNP number is the stable accession regardless of the differences in genomic assemblies. RefSNP numbers facilitate large-scale studies in association genetics, medical genetics, functional and pharmaco-genomics, population genetics and evolutionary biology, personal genomics, and precision medicine. They provide a stable variant notation for mutation and polymorphism analysis, annotation, reporting, data mining, and data integration.