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cgh-processor

Array CGH Signal processor

cip_api_reports

clingen_dosage_sensitivity_bedfile

OBSOLETE: one-off use script used to create a BED file used as a track for array analysis

coverage_boxplots

CovApp is an R shiny app that shows gene coverage boxplots for in-house WES data. In production use but no release / audit

coverage_uniformity_report

Standalone R script and Docker components used by the DNA Nexus App moka-guys/dnanexus_coverage_uniformity_report to calculate uniformity of coverage across multiple samples.

custom_reference

datasets

Datasets that are used (mainly) for the Developmental Disorders array CGH service

decipher_upload

Used to upload variants to Decipher

digital_mlpa

Scripts for supporting the digital MLPA service

dmlpa-flask

Flask frontend to dMLPA dockerised R Scripts

dmlpa-reporting

Report generator for dMPLA

dnanexus_albacore_barcoding

dnanexus_ampliconfilter

NO LONGER IN PROD USE. DNAnexus app running AmpliconFilter v1.0 to remove any alignments which are not the product of an amplicon

dnanexus_amplivar_blat

OBSOLETE: DNAnexus app for analysis of cancer samples - runs amplivar blat from moka-guys/amplivar_blat - robust mutation detection in amplicon-based next generation sequencing (NGS) data

dnanexus_amplivar_coverage

OBSOLETE: DNAnexus app running a Python script which parses output from amplivar and variant calling steps into one document per sample

dnanexus_archival

OBSOLETE

dnanexus_arraybackup

Upload files from the MicroArray scanner PC to DNANexus

dnanexus_automate_multiqc_workflow

dnanexus_bamclipper

OBSOLETE: DNAnexus app running tommyau/bamclipper to softclip primer sequences from aligned data

dnanexus_batch_runner

dnanexus_bcftools_stats

Script input to the DNAnexus swiss army knife app to run bcftools stats

dnanexus_bcl2fastq2

dnanexus_bigwig_coverage_map_report

DNA Nexus App to create bigwig coverage maps from the stiched/realigned BAMs for TSO runs

dnanexus_bwa

DNAnexus app mapping FASTQ reads (paired or unpaired) to a reference genome with the BWA-MEM algorithm

dnanexus_calculate_common_coverage

OBSOLETE: DNAnexus app running the dockerised moka-guys/calculate_common_coverage script which calculates the % of each gene covered at the required read depth in all samples involved in an analysis

dnanexus_canvas

OBSOLETE: Decision to use exomedepth instead

dnanexus_cnvseq

OBSOLETE: Decision to use exomedepth instead

dnanexus_concat_fastqs

dnanexus_congenica_upload

DNAnexus app for uploading samples to the Congenica analysis platform

dnanexus_convert_to_rpkm_bedfile

SUPERSEDED BY EXOME DEPTH. DNANexus app creating bedfiles suitable for use with the DNA nexus RPKM app