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100k_check_labkey

Gets data from the Genomics England LabKey API for a given participant ID

100k_exit_questionnaire

Auto create Summary of Findings + Exit Questionnaire payloads for Neg Neg reports and send via the CIP API¶

100k_moka_booking_in

Parses the ouput from 100k_negnegs/negneg_cases.py and creates NGStest requests in Moka for all cases (not just negnegs) that are not already in Moka

100k_moka_variants

100k_negnegs

Retrieves Guy's 100k cases from CIP-API that are ready for interpretation and groups them based on whether they are negative negative or not

100k_patients_geneworks

Pulls patient information from Geneworks for interpretation requests in GeL results email

100k_summary_findings_pdf

Downloads the summary of findings html for a 100k case, performs some minor reformatting and converts it to a pdf

100k_tracking

161216_rerun_coverage_sambamba

add_ref_build_to_vcf

OBSOLETE: Never used. Script called by Swiss Army app in MokaONC - adds line to VCF headers specifying reference as hg19

adhoc_scripts

Scripts for adhoc changes. See readme for details of each script

agilent_array_design_files

OBSOLETE

agilent_bravo_program_files

OBSOLETE

ampliconfilter

NO LONGER IN PROD USE. Scripts to mask or softclip primers in aligned DNA amplicons

amplivar

OBSOLETE: Grouped Read Testing

amplivar_blat

OBSOLETE: Tool for robust mutation detection in amplicon-based next generation sequencing (NGS) data designed for use in clinical diagnostic setting (uses code from moka-guys/amplivar)

appauth

Email based application authentication service

archer_archiving

Script for backing up data from the Archer analysis platform to DNAnexus for long term storage

archer_extended_job_report

Script used in the archer analysis software to generate extended job reports

arraybed

arraycgh

OBSOLETE

arraypgd

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

automate_demultiplex

Scripts for routine analysis of clinical next generation sequencing (NGS) data at Synnovis Genetics

automatecoveragereports

Import coverage to the moka database. batch_insert.py is used to insert coverage reports into Moka for WES samples

batch_vcf_verifier

Compares a batch of truth VCFs to a batch of query VCFs to verify genomic pipelines

bedfile_editor

Django web tool to create, edit, and view bedfile data for clinical applications

bedmakercli

A suite of CLI tools fro creating bed files

benchmarking_tool

Django benchmarking tool webapp

bp_genomics_export

OBSOLETE: Was used to pull together data into a required format for the WES service that was outsourced to blueprint genomics