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/automate_demultiplex
Scripts for routine analysis of clinical next generation sequencing (NGS) data at Synnovis Genetics
moka-guys/dnanexus_ED_cnv_calling
Performs CNV calling using ExomeDepth.
moka-guys/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
moka-guys/moka-fe
This repo is incomplete and serves as a backup of some code from Moka. It includes some legac(hitt)y code.
moka-guys/adhoc_scripts
Scripts for adhoc changes. See readme for details of each script
moka-guys/archer_archiving
Script for backing up data from the Archer analysis platform to DNAnexus for long term storage
moka-guys/dMLPA-flask
Flask frontend to dMLPA dockerised R Scripts
moka-guys/archer_api_upload
moka-guys/bedmakerGUI
moka-guys/dnanexus_archer_api_upload
moka-guys/dnanexus_arraybackup
Upload files from the MicroArray scanner PC to DNANexus
moka-guys/dnanexus_duty_csv
DNAnexus implementation of duty_csv. To be used in conjunction with process_duty_csv
moka-guys/dnanexus_ED_readcount_analysis
This app calculates the readcount for a batch of samples for CNV calling using ExomeDepth.
moka-guys/dnanexus_happy
DNAnexus app comparing a query VCF to a truth VCF to calculate performance metrics including sensitivity and precision using hap.py and vcfeval
moka-guys/dnanexus_mokapipe_workflow
Workflow description of DNANexus workflow GATK3.5
moka-guys/dnanexus_oncodeep_upload
moka-guys/dnanexus_scip_mpileup
Modified version of dnanexus_mpileup to do some extra data manipulation on scip patient data
moka-guys/dnanexus_upload_multiqc
App to upload multiqc files to genomics server
moka-guys/duty_csv
Generates a CSV file containing DNAnexus download links for end of run processing. To be used in conjunction with process_duty_csv
moka-guys/fhprs
FH Polygenic risk score
moka-guys/get_DNAnexus_URLs
Generates a .json containing URLs for VCF, BAM and index files located on DNAnexus for use in the IGV browser
moka-guys/igvwebapp
Docker build for the IGV WebApp
moka-guys/integrity_checking
Script to display a message box on the sequencers, with the goal of ensuring data is not lost should the data integrity check fail
moka-guys/mokabed
Generates BED files
moka-guys/samplesheet_validator
A package to validate the formatting of Illumina SampleSheets and which notifies the user of any issues
moka-guys/SCIP
moka-guys/SNP_haplotyper
BASHer (BiAllellic SNP Haplotyper). This script filters and classifies SNPs for SNP Array data
moka-guys/sophiaCLI_automate
AOI script for automation of Sophia CLI requests
moka-guys/workstation_crontab
moka-guys/workstation_housekeeping
Scripts to manage data on the NGS workstation