Discover eastgenomics/cp_upload Open Source project

Stars
1
Language
Shell
Created about 4 years ago
Updated about 4 years ago

eastgenomics

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Script to perform setup for uploading CP data 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

array_backup

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

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

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/cp_upload

eastgenomics

Reviews

Repository Details

More Repositories