Repositories list

• pprs-pipeline

  Public
  Paritioned Polygenic Risk Scores pipeline: essentially a wrapper around `plink --score` which automatically finds proxies for missing variants using LDlinkR.

  R

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• primed_consortia_legacy_project_phenotypes

  Public
  Code to create lists of EMR codes for Biobanks to use in the NHGRI's PRIMED Consortium Legacy Project

  HTML

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• polygenic-risk-scores-pipeline

  Public
  Pipeline to calculate polygenic risk scores from VCF files

  Shell

  •0•3•1•0•Updated Nov 25, 2024Nov 25, 2024

• metabolomics-qc

  Public
  R

  •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• primed_consortia_legacy_benchmarking_project

  Public
  0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

• fetch-dbgap-data-workflow

  Public
  WDL

  •1•2•0•0•Updated Sep 18, 2024Sep 18, 2024

• subset-gds

  Public
  Uses the uwgac/topmed-master docker images to uses SeqArray

  WDL

  •0•0•0•0•Updated Jul 6, 2022Jul 6, 2022

• topmed-t2d-wg-trait-harmonization

  Public
  repo for all trait harmonization related files in topmed t2d/glycemic traits

  HTML

  •1•1•1•0•Updated Mar 25, 2022Mar 25, 2022

• subset-vcf-workflow

  Public
  WDL

  •0•0•0•0•Updated Dec 1, 2021Dec 1, 2021

• regenie-workflow

  Public
  Common Workflow Language

  •0•0•0•0•Updated Nov 29, 2021Nov 29, 2021

• vcfToGds

  Public
  Convert Vcf files to Gds format

  WDL

  •

  MIT License

  •4•4•1•0•Updated Oct 6, 2021Oct 6, 2021

• neural-admixture

  Public
  Python

  •9•0•0•0•Updated Aug 18, 2021Aug 18, 2021

• WGSAssociationVisualization

  Public
  R

  •1•1•0•0•Updated Jul 30, 2021Jul 30, 2021

• custom_terra_images

  Public
  0•0•0•0•Updated Jul 23, 2021Jul 23, 2021

• GIL

  Public
  Generalized image learning - DL pipeline for BDCatalyst powered by Seven Bridges

  Python

  •2•0•0•0•Updated Jul 20, 2021Jul 20, 2021

• ukb-covid-gxe

  Public
  HTML

  •0•0•0•0•Updated Jun 29, 2021Jun 29, 2021

• hla-prs-toolkit

  Public
  Toolkit to aid generation of advanced Polygenic Risk Scores (PRS) including SNP-allele tagging and interaction models, especially in HLA. Developed and maintained by Seth Sharp ([email protected]).

  Shell

  •

  GNU General Public License v3.0

  •5•0•0•0•Updated May 27, 2021May 27, 2021

• subset-genotypes-workflow

  Public
  WDL

  •0•0•0•0•Updated Dec 24, 2020Dec 24, 2020

• singleVariantAssociation

  Public
  Single variant association workflow (mixed models in GENESIS)

  R

  •

  MIT License

  •0•2•2•0•Updated Mar 16, 2020Mar 16, 2020

• ldsc_wdl

  Public
  WDL workflow for running LD Score Regression

  Python

  •

  MIT License

  •2•0•0•1•Updated Mar 3, 2020Mar 3, 2020

• WGSregionalPlot

  Public
  Regional plots for WGS summary statistics

  R

  •0•0•0•0•Updated Aug 29, 2019Aug 29, 2019

• variantResults

  Public
  Tools for exploring single and aggregate variant results

  R

  •

  MIT License

  •0•0•0•0•Updated Apr 26, 2019Apr 26, 2019

• aggregateAssociation

  Public
  Genesis workflow for SKAT/Burden testing

  R

  •

  MIT License

  •0•1•1•0•Updated Feb 26, 2019Feb 26, 2019

• metal

  Public
  WDL wrapper and docker image for running Metal meta-analysis software.

  R

  •

  MIT License

  •0•3•0•0•Updated Aug 17, 2018Aug 17, 2018

• glmAssociation

  Public
  linear/logistic/firth for single variant association

  R

  •0•0•0•0•Updated Aug 17, 2018Aug 17, 2018

• wgsaParsrWdl

  Public
  WDL wrapper for UW-GAC wgsaParsr tool

  WDL

  •

  MIT License

  •0•1•0•0•Updated Aug 1, 2018Aug 1, 2018

• fitNull

  Public
  Fit a null model in Genesis

  WDL

  •

  MIT License

  •0•0•0•0•Updated Aug 1, 2018Aug 1, 2018

• fineMap

  Public
  Pipelines for fine mapping in genetic association analysis

  Python

  •

  MIT License

  •0•1•1•0•Updated Aug 1, 2018Aug 1, 2018

• topmed-t2d-glycemia-public

  Public
  Scripts, docker images and pipelines for analysis by the TOPMed Diabetes working group

  HTML

  •1•0•6•1•Updated Jul 23, 2018Jul 23, 2018

• saigeWdl

  Public
  wdl wrapper for the SAIGE tool

  WDL

  •

  MIT License

  •0•1•0•0•Updated Apr 5, 2018Apr 5, 2018