Discover eastgenomics/array_backup Open Source project

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eastgenomics

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scripts to run monthly to backup 750k array data from the array PC to DNAnexus

eggd_tso500

Runs the Illumina TSO500 local analysis app.

Shell

eggd_mosdepth

mosdepth (DNAnexus Platform App)

Shell

eggd_staraligner

Shell

Ploutos

Code for the DNAnexus billing project.

Python

code_school

HTML

eggd_pandora

Python

themis

Code for internal bioinformatics team auditing

Python

validate_sample_sheet

Validates Illumina SampleSheet for bcl2fastq / bclconvert

Python

eggd_generate_variant_workbook

DNAnexus app for generating xlsx variant workbooks

Python

athena

Provides HTML reports with detailed coverage analysis for clinical NGS data.

HTML

automated-archiving

Python script to monitor archiving on DNANexus

Python

exon_file_and_g2t_from_new_refseq_gff

Scripts to convert refseq gff to tsv and convert that tsv into a g2t file

Python

egg1_dias_TSO_config

Config for the Dias TSO assay

Python

eggd_starfusion

Shell

opencga_data_upload

Python

eggd_additional_cnv_tasks

Adds CNV length value to vcf and creates visualisation seg file

Python

eggd_fusioninspector

Shell

eggd_nirvana2vcf

Converts a nirvana json into a VEP style annotated vcf

Python

eggd_dias_single_workflow

Workflow definition for Dias single

convert_variant_format

eggd_vcf_rescue

Shell

TSO500Reporter

Python

egg5_dias_CEN_config

eggd_somalier_extract

Shell

eggd_uranus_main_workflow

DNAnexus Uranus workflow to support the Haem-Onc myeloid project

eggd_vcf_header_corrector

App to adjust the headers of VCF files produced by Mutect2 and cpgPindel.

Shell

test_directory_parser

Script(s) to parse the test directories

Python

run_dx_checker

Runs workflow for eggd_dx_checker

Python

g2t_ops

Operations relating to genes and transcripts

Python

panel_ops

Panel database related operations

Python

eggd_iva_upload

Push data to IVA

Shell

dnanexus_swiss_army_remove_germline_risk

Shell

CNV_calling_dev

GATK 4 germlineCNVcaller

Shell

eggd_somalier_workflow

check_nirvana_genes2transcripts

Check the transcripts selected in genes2transcripts against those available in Nirvana Cache

Python

eggd_dias_cnvreports_workflow

eggd_vcf_handler_for_uranus

Python

sWGS_batch

Collection of scripts to start batch jobs for sWGS

egg4_dias_TWE_config

Config for the Dias TWE assay

panel_prep

Python

push_to_decipher

eggd_GATKgCNV_prep

Shell

nirvana_gff_to_bed

Converts a nirvana cache RefSeq gff file into a bed file

Python

cancer_directory

Interactive version of national cancer test directory

eggd_vep_CEN_config

Json configuration file for the implementation of VEP for the CEN assay.

eggd_pbtp_url_generator

Produces time-limited reporting URLs for a list of PBTP samples.

Shell

CRAM_TO_FASTQ

Shell

pull_from_opencga

gene_annotation2bed

Python

ManeCheck

generate_manifest

Generate a sample/panel manifest from samples and genepanels database dumps

CRAM_Conversion_v1.0

panel_comparison

eggd_conductor

DNAnexus app for automated analysis

Python

eggd_dx_checker

App to check for effects of weekly DNAnexus updates

Shell

ngc_vep

eggd_nimagen_to_gel_vcf

Shell

eggd_expected_depth

Python

dx_job_monitor

Check if the 002 jobs completed correctly and sends notifications

Python

eggd_bam2fqs

Convert BAM file to fastqs

Shell

cp_upload

Script to perform setup for uploading CP data to DNAnexus

Shell

new_repo_template

description of repo

ngc_extract_exonic_region_grch37

Shell

eggd_generate_vcf_metadata

Shell

lab_panels_vs_panelapp_panels

Python

aphrodite_batch

cellbase_annotation

dias_batch_running

Python

dnanexus_swiss_army_pindel_bcftools_filter

Shell

eggd_mosdepth_plots

DNAnexus app to generate coverage plots from mosdepth distribution output

eggd_vcf_annotator

DNAnexus app to annotate vcfs

Shell

OPAtransform

Jupyter notebook used to transform the non-synonymous hotspots list provided by the solid cancer scientists to a vcf

hermes

East Genomics private Slack bot !

Python

dnanexus_swiss_army_cgppindel_bcftools_filter

Filters cgpPindel output vcfs

Shell

eggd_athena

DNAnexus app of Athena

Shell

eggd_confirmation_thresholds

dnanexus app for running confirmation_thresholds (VCF QC Distributions)

ConfirmationThresholds

A tool to plot distributions of VCF metrics separated by TP/FP or sampleID

ansible-run-monitoring

script for monitoring ansible server

Python

eggd_somalier_relate2multiqc

Python

eggd_fastqc

Run fastqc app once for each input fastq

HTML

Haemonc_requests

Python

100KRDActiveList

Python

eggd_bam_cleaner

panel_matching

eggd_sompy

Shell

demo_sentieon_app

Sentieon in DNAnexus app

Shell

ngc_mtoolbox

Shell

eggd_TSO500_reports_workflow

Shell

uranus_batch

eggd_cgppindel

Shell

iscan_to_dnanexus

Transfer iScan data from local server to DNAnexus

Shell

pedigree_file_generator

egg_announce

Testing slackbot to announce releases

eggd_multi_hap.py

Runs happy once for each query vcf

Shell

eggd_zetta_integration_tool

eggd_fqRename

Shell

ngc_smncopynumbercaller

eggd_vep

Shell

eggd_dias_multi_workflow

Workflow definition for Dias multi

100

eris

Python

eastgenomics/array_backup

eastgenomics

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