Pinned Repositories
161216_rerun_coverage_sambamba
arraybed
automate_demultiplex
Scripts for routine analysis of clinical next generation sequencing (NGS) data at Synnovis Genetics
dnanexus_ED_cnv_calling
Performs CNV calling using ExomeDepth.
dnanexus_swiss_army_SNP_bcftools_filter
This repository contains the commands executed by the swiss army knife app (v3.0.0) to format a VCF according to GeL specifications for SNP ID checks
dnanexus_workflows
seglh-cnv
Scripts and docker images to run CNV pipelines
seglh-naming
SEGLH naming schemes
summarise_gene_panel
OBSOLETE: One-off research project, summarising coverage of a set of genes
WGS_puberty_CNVs
Scripts for filtering WGS Puberty SV data
MokaGuys's Repositories
moka-guys/dx_api_bridge
DNAnexus API bridge. Retrieve data object URIs. Manage archival processes and perform cost audits.
moka-guys/seglh-naming
SEGLH naming schemes
moka-guys/WGS_puberty_CNVs
Scripts for filtering WGS Puberty SV data
moka-guys/archer_extended_job_report
Script used in the archer analysis software to generate extended job reports
moka-guys/_CNVkit_DNAnexus_App
Part of MSc project for Igor
moka-guys/appauth
Email based application authentication service
moka-guys/ArraySpiker
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
moka-guys/AutomateCoverageReports
Import coverage to the moka database. batch_insert.py is used to insert coverage reports into Moka for WES samples
moka-guys/bedfile_editor
Django web tool to create, edit, and view bedfile data for clinical applications
moka-guys/digital_mlpa
Scripts for supporting the digital MLPA service
moka-guys/dnanexus_amplivar_coverage
OBSOLETE: DNAnexus app running a Python script which parses output from amplivar and variant calling steps into one document per sample
moka-guys/dnanexus_bigwig_coverage_map_report
DNA Nexus App to create bigwig coverage maps from the stiched/realigned BAMs for TSO runs
moka-guys/dnanexus_filter_vcf_with_bedfile
DNAnexus app to filter variants after variant calling using a BED file
moka-guys/dnanexus_MokaSNP_workflow
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)
moka-guys/dnanexus_polyedge
Determine if a known variant is present at the base preceeding a poly stretch in a BAM file
moka-guys/dnanexus_somalier
Somalier is a tool that can rapidly evaluate relatedness from sequencing data
moka-guys/dnanexus_sompy
This app uses the som.py module from the hap.py package from Illumina. Two VCFs can be compared (e.g. a "truth" VCF against a query) and the recall reported.
moka-guys/dnanexus_tso500_output_parser
DNAnexus app to set off QC steps (DNAnexus apps) for specific files output by the TSO500 app
moka-guys/dnanexus_vardict
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
moka-guys/dnanexus_varscan2
NO LONGER IN PROD USE. DNAnexus app applying Varscan2 (v2.4.3), a variant caller well suited for somatic samples
moka-guys/dnanexus_wes_congenica_sftp_upload
App and bash script for uploading WES samples to Congenica via SFTP
moka-guys/fastqc
FastQC Dockerfile
moka-guys/genomics_server_download
Scripts for downloading files from DNA Nexus to the ArcherDx analysis platform via Genomics server
moka-guys/guidance
Guidance documents that cover coding style, versioning, and documentation of code written in the bioinformatics groups of the South East Genomic Laboratory Hub
moka-guys/polyedge
Finds variants at the edge of a poly that is is varying length
moka-guys/seglh-toolbox
Source code for third party tools that have been verified/validated for use, as docker images
moka-guys/soteria
Samplesheet uploader and validator
moka-guys/undocking
Tools to backup and move images from dockerhub
moka-guys/vcfserver
VCF HTTP server
moka-guys/workflows
WDL based secondary analysis workflows