moka-guys Goto Github PK
Name: MokaGuys
Type: Organization
Name: MokaGuys
Type: Organization
Gets data from the Genomics England LabKey API for a given participant ID
Auto create Summary of Findings + Exit Questionnaire payloads for Neg Neg reports and send via the CIP API¶
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
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
Pulls patient information from Geneworks for interpretation requests in GeL results email
Downloads the summary of findings html for a 100k case, performs some minor reformatting and converts it to a pdf
OBSOLETE: Never used. Script called by Swiss Army app in MokaONC - adds line to VCF headers specifying reference as hg19
Scripts for adhoc changes. See readme for details of each script
OBSOLETE
OBSOLETE
NO LONGER IN PROD USE. Scripts to mask or softclip primers in aligned DNA amplicons
OBSOLETE: Grouped Read Testing
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)
Email based application authentication service
Script for backing up data from the Archer analysis platform to DNAnexus for long term storage
Script used in the archer analysis software to generate extended job reports
OBSOLETE
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
Scripts for routine analysis of clinical next generation sequencing (NGS) data at Synnovis Genetics
Import coverage to the moka database. batch_insert.py is used to insert coverage reports into Moka for WES samples
Compares a batch of truth VCFs to a batch of query VCFs to verify genomic pipelines
Django web tool to create, edit, and view bedfile data for clinical applications
A suite of CLI tools fro creating bed files
Django benchmarking tool webapp
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