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@AWGL All Wales Medical Genomics Service

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    58 repositories

    • DragenWGS

      Public
      A pipeline for analysing WGS data on the Dragen
      Shell
      •2•6•0•1•Updated Jul 10, 2026Jul 10, 2026

    • TSO500_post_processing

      Public
      Python
      •0•0•3•2•Updated Jun 1, 2026Jun 1, 2026

    • DragenGE

      Public
      Pipeline for joint calling of samples from targeted enrichment assays.
      Shell
      •0•1•0•1•Updated May 7, 2026May 7, 2026

    • IlluminaQC-WREN

      Public
      Shell
      •1•0•2•0•Updated Apr 21, 2026Apr 21, 2026

    • CoverageCalculatorPy

      Public
      Calculated coverage metrics from a GATK3 Depth Of Coverage file and a bedfile
      Python
      •0•1•1•1•Updated Dec 31, 2025Dec 31, 2025

    • cancer_uom

      Public
      Uncertainty of measurement calculations for cancer NGS
      Python
      •0•0•1•1•Updated Nov 4, 2025Nov 4, 2025

    • SomaticAmplicon

      Public
      NGS pipeline for somatic variant calling from amplicon datasets
      Shell
      •2•0•0•0•Updated Oct 14, 2025Oct 14, 2025

    • DragenQC

      Public
      Pipeline to Demultiplex and initiate downstream pipelines on the Dragen server
      Shell
      •0•0•1•0•Updated Oct 14, 2025Oct 14, 2025

    • read_count_data_visualisation

      Public
      A script for visualising read count data for TSO500 runs.
      Python
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • pdf_scanner

      Public
      searches all PDF files in a directory for a given string
      Python
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • bad_code

      Public
      A repository of bad code for code review teaching
      Python
      •0•0•0•0•Updated May 14, 2025May 14, 2025

    • copy_tsca

      Public
      Copying files for TruSight Cancer workflow
      Python
      •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • somalier_wrapper

      Public
      wrapper scripts for estimating relatedness between samples using the software Somalier
      1•0•0•1•Updated Oct 25, 2024Oct 25, 2024

    • variant_classification_DB

      Public archive
      A database for storing the classification of variants.
      Python
      •2•5•10•0•Updated Sep 17, 2024Sep 17, 2024

    • vcf_parse

      Public
      Python script for parsing VCF files and making a text report.
      Python
      •0•0•0•1•Updated Aug 10, 2023Aug 10, 2023

    • filter_potential_mosaics

      Public
      Expanded filter for use with GermlineEnrichment pipeline output when a mosaic variant is suspected
      Python
      •0•0•0•0•Updated Mar 21, 2023Mar 21, 2023

    • NIPD

      Public
      Non Invasive Prenatal Diagnosis - Variant Calling Pipeline and Analysis Software
      snakemakepandasprenatal
      snakemakepandasprenatalnipd
      0•1•2•0•Updated Dec 7, 2021Dec 7, 2021

    • VirtualHood

      Public archive
      Python
      •0•0•0•0•Updated Aug 4, 2021Aug 4, 2021

    • triplet_repeat_automation

      Public
      Python
      •1•0•0•0•Updated Jul 9, 2021Jul 9, 2021

    • SomaticEnrichment

      Public archive
      NGS pipeline for the detection of somatic variation (SNVs & CNVs) and fusion genes
      Shell
      •1•1•3•0•Updated Jul 5, 2021Jul 5, 2021

    • cruk_pipeline

      Public archive
      Python
      •0•0•4•0•Updated Jun 22, 2021Jun 22, 2021

    • SomaticFusion

      Public archive
      Python
      •1•0•1•0•Updated May 19, 2021May 19, 2021

    • ngs_run_summary

      Public
      Python
      •1•0•0•0•Updated May 13, 2021May 13, 2021

    • bed2hgvs-1

      Public
      Annotates a BED file with HGVS-like coordinates
      R
      •
      MIT License
      •1•0•0•0•Updated Dec 11, 2020Dec 11, 2020

    • DragenInfrastructure

      Public
      General Scripts needed for the Dragen Server
      Shell
      •0•0•1•0•Updated Oct 13, 2020Oct 13, 2020

    • IlluminaQC

      Public archive
      Shell script for BCL to uBAM, QC and analysis launch
      Shell
      •3•0•0•0•Updated Jul 1, 2020Jul 1, 2020

    • GermlineEnrichment

      Public archive
      Variant calling pipeline for germline enrichment NGS data
      Shell
      •3•0•0•0•Updated Jun 12, 2020Jun 12, 2020

    • query_shire

      Public archive
      0•0•0•0•Updated Feb 27, 2020Feb 27, 2020

    • sample_sheets

      Public archive
      0•0•0•0•Updated Feb 27, 2020Feb 27, 2020

    • NGS_Sample_Sheets

      Public archive
      Sample sheet generator to run samples on NGS machines
      Java
      •
      MIT License
      •0•1•0•0•Updated Jan 20, 2020Jan 20, 2020
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