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    101 repositories

    • workstation_housekeeping

      Public archive
      Scripts to manage data on the NGS workstation
      workstation
      Python
      •
      Other
      •1•0•10•1•Updated Jul 5, 2024Jul 5, 2024

    • dnanexus_vardict

      Public archive
      NO LONGER IN PROD USE. DNAnexus app performing variant calling using the VarDict variant caller, calling SNV, MNV, indels (<120 bp default), and complex variants
      Perl
      •0•0•4•0•Updated May 5, 2023May 5, 2023

    • dnanexus_varscan2

      Public archive
      NO LONGER IN PROD USE. DNAnexus app applying Varscan2 (v2.4.3), a variant caller well suited for somatic samples
      Shell
      •0•0•3•0•Updated Feb 20, 2023Feb 20, 2023

    • dnanexus_bigwig_coverage_map_report

      Public archive
      DNA Nexus App to create bigwig coverage maps from the stiched/realigned BAMs for TSO runs
      GNU General Public License v3.0
      •0•0•0•1•Updated Feb 3, 2023Feb 3, 2023

    • dnanexus_tso500_output_parser

      Public archive
      DNAnexus app to set off QC steps (DNAnexus apps) for specific files output by the TSO500 app
      Shell
      •0•0•0•0•Updated Jan 13, 2023Jan 13, 2023

    • AutomateCoverageReports

      Public archive
      Import coverage to the moka database. batch_insert.py is used to insert coverage reports into Moka for WES samples
      Python
      •0•0•9•0•Updated Dec 20, 2022Dec 20, 2022

    • ArraySpiker

      Public archive
      Script run during the analysis of Agilent CGH Array results. It compares the expected presence of spiked in probes to that detected, flagging any mismatch to the user
      Python
      •0•0•0•8•Updated Dec 8, 2022Dec 8, 2022

    • dnanexus_amplivar_coverage

      Public archive
      OBSOLETE: DNAnexus app running a Python script which parses output from amplivar and variant calling steps into one document per sample
      Python
      •1•0•1•1•Updated Oct 14, 2022Oct 14, 2022

    • _CNVkit_DNAnexus_App

      Public archive
      Part of MSc project for Igor
      0•0•0•0•Updated Aug 15, 2022Aug 15, 2022

    • dnanexus_MokaSNP_workflow

      Public archive
      OBSOLETE: Workflow description of DNANexus workflow 'SNP Genotyping' (genotypes a set of SNPs to be uploaded to the sample matching service for the GMS WGS)
      0•0•3•0•Updated May 20, 2022May 20, 2022

    • project_requirements

      Public archive
      Project requirement document templates
      0•0•0•1•Updated Mar 15, 2022Mar 15, 2022

    • dnanexus_archival

      Public archive
      OBSOLETE
      Python
      •0•0•0•0•Updated Jan 5, 2022Jan 5, 2022

    • dnanexus_ampliconfilter

      Public archive
      NO LONGER IN PROD USE. DNAnexus app running AmpliconFilter v1.0 to remove any alignments which are not the product of an amplicon
      Shell
      •0•0•1•0•Updated Nov 17, 2021Nov 17, 2021

    • ampliconfilter

      Public archive
      NO LONGER IN PROD USE. Scripts to mask or softclip primers in aligned DNA amplicons
      Python
      •
      MIT License
      •0•0•1•0•Updated Nov 17, 2021Nov 17, 2021

    • dnanexus_mokaamp_workflow

      Public archive
      NO LONGER IN PROD USE. Workflow description of DNANexus workflow MokaAMP
      0•0•0•0•Updated Oct 11, 2021Oct 11, 2021

    • 100K_exit_questionnaire

      Public archive
      Auto create Summary of Findings + Exit Questionnaire payloads for Neg Neg reports and send via the CIP API¶
      Python
      •0•0•4•0•Updated Oct 3, 2021Oct 3, 2021

    • arraycgh

      Public archive
      OBSOLETE
      Python
      •0•0•0•0•Updated Oct 3, 2021Oct 3, 2021

    • RPKM

      Public archive
      SUPERSEDED BY EXOME DEPTH. Tools used to generate RPKM data from BAM files. Makes use of Conifer CF_bam2RPKM function to generate RPKM. Contains a wrapper script called rpkmanalysis.py which processes a list of BAMs and outputs RPKM text files to a specific output folder.
      Python
      •
      GNU General Public License v3.0
      •0•0•3•0•Updated Oct 3, 2021Oct 3, 2021

    • BP_genomics_export

      Public archive
      OBSOLETE: Was used to pull together data into a required format for the WES service that was outsourced to blueprint genomics
      Python
      •0•0•0•0•Updated Oct 3, 2021Oct 3, 2021

    • dnanexus_mokawes_workflow

      Public archive
      OBSOLETE: Workflow description of DNANexus workflow MokaWES
      0•0•0•0•Updated Oct 3, 2021Oct 3, 2021

    • calculate_common_coverage

      Public archive
      OBSOLETE: Script calculates the % of each gene covered at the required read depth in all samples involved in an analysis
      Python
      •0•0•0•0•Updated Oct 3, 2021Oct 3, 2021

    • dnanexus_mokaonc_workflow

      Public archive
      Workflow description of DNANexus workflow MokaONC. Replaced by MokaAMP
      Shell
      •0•0•0•0•Updated Oct 1, 2021Oct 1, 2021

    • 100k_moka_variants

      Public archive
      Python
      •0•0•4•0•Updated Oct 1, 2021Oct 1, 2021

    • dnanexus_RPKM

      Public archive
      SUPERSEDED BY EXOME DEPTH. DNAnexus app that uses moka-guys/RPKM to perform RPKM analysis
      Shell
      •0•0•1•0•Updated Oct 1, 2021Oct 1, 2021

    • dnanexus_smartsheet_mokapipe_complete

      Public archive
      OBSOLETE: Updates smartsheet to mark completion of MokaPipe
      Python
      •0•0•1•0•Updated Oct 1, 2021Oct 1, 2021

    • dnanexus_picard

      Public archive
      Shell
      •0•0•1•0•Updated Sep 7, 2021Sep 7, 2021

    • dnanexus_MokaCAN_workflow

      Public archive
      Workflow description of DNANexus workflow MokaCAN
      0•0•4•0•Updated Jul 26, 2021Jul 26, 2021

    • dnanexus_vcfeval

      Public archive
      OBSOLETE - superseded by happy. DNAnexus app calculating sensitivity and specificity using the NA12878 HapMap sample
      Shell
      •0•0•2•0•Updated Feb 24, 2021Feb 24, 2021

    • Add_ref_build_to_vcf

      Public archive
      OBSOLETE: Never used. Script called by Swiss Army app in MokaONC - adds line to VCF headers specifying reference as hg19
      0•0•0•0•Updated Feb 9, 2021Feb 9, 2021

    • GeL_Reports

      Public archive
      Creates cover page for the summary of findings downloaded from GeL, used for cases that do not require a Geneworks report
      Python
      •0•0•7•0•Updated Sep 24, 2020Sep 24, 2020
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