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    37 repositories

    • clinical-filtering

      Public
      Python
      •1•0•0•0•Updated Aug 11, 2025Aug 11, 2025

    • outlier-exclusion

      Public
      Workflows for filtering gATK-SV callsets
      WDL
      •1•0•1•1•Updated Aug 9, 2025Aug 9, 2025

    • lr-annotation

      Public
      Tools for callset annotation in long-read cohorts.
      WDL
      •
      MIT License
      •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

    • variant-interpretation

      Public
      WDL
      •7•5•0•0•Updated Aug 4, 2025Aug 4, 2025

    • preprocessing

      Public
      WDL
      •0•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • annotations

      Public
      WDL
      •1•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • denovo-snv-indels

      Public
      Python
      •1•0•0•0•Updated Jul 17, 2025Jul 17, 2025

    • gCNV-analysis-tools

      Public
      Analysis tools for gCNV
      R
      •1•0•3•0•Updated Jul 14, 2025Jul 14, 2025

    • sva_typer

      Public
      A tool for genotyping SVA elements and substructure
      Rust
      •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • gatk-sv-internal

      Public
      Miscellaneous workflows and scripts for GATK-SV
      WDL
      •1•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • dsmap

      Public
      Shell
      •
      MIT License
      •1•0•2•0•Updated Mar 25, 2025Mar 25, 2025

    • athena

      Public
      Toolkit for structural variation mutation rates and dosage sensitivity
      Python
      •
      MIT License
      •0•0•2•0•Updated Feb 4, 2025Feb 4, 2025

    • cnv-validation

      Public
      WDL
      •1•0•0•1•Updated Oct 8, 2024Oct 8, 2024

    • SMC_CNN_Model

      Public
      Pipelines to reproduce analysis result for the SMC new target paper
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 23, 2024Jun 23, 2024

    • count_variant_occurrence

      Public
      WDL
      •
      MIT License
      •1•0•0•0•Updated Jun 17, 2024Jun 17, 2024

    • pzm

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 10, 2024Jun 10, 2024

    • 1kgp-gatk-sv-test

      Public
      Test GATK-SV on 1KGP Subset
      WDL
      •
      MIT License
      •0•0•0•0•Updated Apr 24, 2024Apr 24, 2024

    • gCNV-QC-Update

      Public
      Update to the gCNV QC step
      R
      •0•0•0•0•Updated Apr 4, 2024Apr 4, 2024

    • PlotCritic

      Public
      Python deployment tool for bespoke image curation projects, oriented toward scientific projects. Please cite https://academic.oup.com/gigascience/article/7/7/giy064/5026174
      Shell
      •
      MIT License
      •3•0•0•0•Updated Aug 17, 2023Aug 17, 2023

    • rWGCNA

      Public
      Resampled consensus WGCNA
      R
      •1•3•0•0•Updated May 4, 2023May 4, 2023

    • rCNV2

      Public
      Aggregation and analyses of rare CNVs across diseases
      R
      •
      MIT License
      •4•14•1•0•Updated Jan 25, 2023Jan 25, 2023

    • gnomad-sv-v3-qc

      Public
      Fork of GATK-SV repo from June 10, 2021, for gnomAD-SV v3 filtering, QC, and post-processing
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •77•0•0•0•Updated Oct 7, 2022Oct 7, 2022

    • TADA_2022

      Public
      R
      •3•1•1•0•Updated May 24, 2022May 24, 2022

    • svtk

      Public archive
      Python
      •12•35•18•0•Updated Mar 2, 2021Mar 2, 2021

    • gnomad-sv-pipeline

      Public archive
      Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
      R
      •
      MIT License
      •14•36•3•0•Updated Jun 19, 2020Jun 19, 2020

    • gatk4-exome-analysis-pipeline

      Public
      This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •42•0•0•0•Updated Jan 13, 2020Jan 13, 2020

    • Holmes

      Public
      Pipeline for structural variation detection from liWGS libraries
      Shell
      •
      MIT License
      •0•5•0•0•Updated Jan 10, 2020Jan 10, 2020

    • gatk4-data-processing

      Public
      Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •78•0•0•0•Updated Oct 16, 2019Oct 16, 2019

    • gatk4-germline-snps-indels

      Public
      Workflows for germline short variant discovery with GATK4
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •57•0•0•0•Updated Jul 18, 2019Jul 18, 2019

    • CommonMind-SV

      Public
      Shell
      •0•0•0•0•Updated Mar 25, 2019Mar 25, 2019