Repositories list

• Regenie_nextflow

  Public
  Pipeline implementation of Regenie

  Nextflow

  •1•3•0•0•Updated Nov 11, 2024Nov 11, 2024

• CARTaGENE_flagship_paper

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

• glimpse_pipeline

  Public
  Pipeline for variant imputation in low depth sequencing data using GLIMPSE

  pipelinegeneticssequencing+ 3glimpsewgs-datagenotype-imputation

  Nextflow

  •

  MIT License

  •1•3•1•0•Updated Aug 28, 2024Aug 28, 2024

• scripts

  Public
  Various scripts

  genetics

  Python

  •2•4•0•0•Updated Aug 20, 2024Aug 20, 2024

• WEGS_pipelines

  Public
  Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

  snpsgeneticssequencing+ 6gatkwgswesindelssnvswegs

  Nextflow

  •

  MIT License

  •0•3•0•0•Updated Jul 16, 2024Jul 16, 2024

• verifybam_pipeline

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Jul 8, 2024Jul 8, 2024

• vep_pipeline

  Public
  Pipeline for variant annotation using Variant Effect Predictor (VEP)

  gwaspipelinenextflow+ 7geneticsannotationsvariantvepvariant-annotationvariant-effect-predictionvep-annotation

  Jupyter Notebook

  •2•5•0•0•Updated Jun 26, 2024Jun 26, 2024

• SV_calling_pipeline

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated May 17, 2024May 17, 2024

• Phenotype_Filtering_Tool

  Public
  Python

  •1•1•1•0•Updated May 14, 2024May 14, 2024

• CARTaGENE_PheWeb

  Public
  A tool to build a website to browse hundreds or thousands of GWAS.

  Python

  •

  MIT License

  •67•0•0•0•Updated Apr 2, 2024Apr 2, 2024

• HGDP_1KG_ancestry_inference

  Public
  Python

  •0•3•0•0•Updated Mar 27, 2024Mar 27, 2024

• bravo_data_prep

  Public
  Work flows and tools to create data that backs the BRAVO API.

  C++

  •

  MIT License

  •2•0•0•0•Updated Feb 12, 2024Feb 12, 2024

• BQC19_Imputation_Panel

  Public
  Nextflow

  •0•1•0•0•Updated Dec 7, 2023Dec 7, 2023

• bravo_api

  Public
  Server side data processing and retrieval endpoints for BRAVO

  Python

  •

  MIT License

  •2•0•0•0•Updated Oct 24, 2023Oct 24, 2023

• AccessibilityMask

  Public
  Python

  •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

• ProgrammingClub

  Public
  MIT License

  •0•0•0•0•Updated Jun 20, 2023Jun 20, 2023

• CARTaGENE_Imputation_Panel

  Public
  Nextflow

  •0•0•0•0•Updated Apr 17, 2023Apr 17, 2023

• WEGS_paper

  Public
  This repository contains source code for the tables and figures presented in the WEGS paper.

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Apr 5, 2023Apr 5, 2023

• shapeit4_pipeline

  Public
  Pipeline for genotype phasing using SHAPEIT4

  pipelinegeneticsphasing+ 1genotype-phasing

  Nextflow

  •

  MIT License

  •0•1•0•0•Updated Mar 24, 2023Mar 24, 2023

• beagle_phasing

  Public
  Nextflow pipeline around Beagle phasing/imputation tool

  Nextflow

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

• RFMix2_local_ancesty

  Public
  Nextflow

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

• skills_test_3

  Public
  1•3•0•0•Updated Aug 27, 2021Aug 27, 2021

• skills_test_2

  Public
  1•4•0•0•Updated Aug 20, 2021Aug 20, 2021

• ExomePLUS_benchmark

  Public
  R

  •0•0•0•0•Updated Dec 22, 2020Dec 22, 2020

• skills_test_1

  Public
  2•0•0•0•Updated Nov 12, 2020Nov 12, 2020