dias_CEN_config_GRCh37_v3.2.0.json

This repo contains a JSON config file which is used with eggd_dias_batch to specify inputs for running the Dias pipeline for CEN data.

What does the config do?

eggd_dias_batch (https://github.com/eastgenomics/eggd_dias_batch) is a DNAnexus app that runs the Dias pipeline for germline sequence data analysis. The egg5_dias_CEN_config repo contains the dias_CEN_config file that specifies the executables and their input files to be used in the Dias pipeline for analysing CEN data on build GRCh37.

New versions of apps and app inputs for use in the Dias pipeline can be updated in the config without needing to update the pipeline itself.

Parts of the config

The config specifies app IDs and workflow IDs at the top, followed by a reference_files dict for inputs common to multiple running modes. The modes section specifies inputs specific to a running mode:

• cnv_call
  • specifies inputs for CNV calling.
• snv_reports
  • specifies inputs for dias_reports.
• cnv_reports
  • specifies inputs for dias_cnvreports.
• mosaic_reports
  • specifies inputs for dias_reports for mosaic reports.
• artemis
  • specifies inputs for artemis

Versions of workflows, apps, and dynamic files in the config

Workflows:

• Dias reports: dias_reports_v2.2.2
  • DNAnexus workflow ID: workflow-GkbJY284FpfgqF8ggz57fVY2
• Dias CNV reports: dias_cnvreports_v1.2.0
  • DNAnexus workflow ID: workflow-Gj77F9041Ky3Vp045gpKx0B4

Apps:

• CNV calling app: eggd_GATKgCNV_call
  • v1.0.2
  • DNAnexus app ID: app-GZ4pXxj4xG062Bj5zjgP1Bb0
• Artemis app: eggd_artemis
  • v1.5.0
  • DNAnexus app ID app-GkbJ7p0463bjk9VKv3x8G5F8

Dynamic files:

File	File name	DNAnexus file ID
genepanels	241024_genepanels.tsv	file-GvJ5fbQ4qQYq73gjGyP57zFB
exons	GCF_000001405.25_GRCh37.p13_genomic.exon_5bp_v2.0.0.tsv	file-GF611Z8433Gk7gZ47gypK7ZZ
genes2transcripts	240402_g2t.tsv	file-Gj770X8433Gb506pjq1PxXG9
exons_with_symbols for eggd_athena	GCF_000001405.25_GRCh37.p13_genomic.symbols.exon_5bp_v2.0.0.tsv	file-GF611Z8433Gf99pBPbJkV7bq
cen_vep_config for SNV/mosaic reports	cen_vep_config_v1.1.20.json	file-GvJ50fQ4z6j0Y26YBVB9Pj06
cen_vep_config for CNV reports	cen-cnv_config_v1.1.0.json	file-GQGJ3Z84xyx0jp1q65K1Q1jY
panel_dump for eggd_optimised_filtering	241030_panelapp_dump.json	file-GvVg3qj4Y54jBF8bgX62gkfQ
additional_regions for CNVs	CEN_CNV_additional_regions_b37_v1.0.1.tsv	file-GJZQvg0433GkyFZg13K6VV6p
additional_regions for SNVs	CEN_SNV_additional_regions_b37_v1.0.0.tsv	file-Gpy96q04PKYjjg9kbQy692bF
gatk_docker	GATK_v4.2.5.0.tar.gz	file-GBBP9JQ433GxV97xBpQkzYZx
interval_list for CNV calling	CEN_CNV_targets_v1.1.0_sorted.interval_list	file-GFPxzKj4V50pJX3F4vV58yyg
annotation of interval_list for CNV calling	CEN_CNV_targets_v1.1.0_sorted_annotation.tsv	file-GFPxzPQ4V50z4pv230p82G0q
capture_bed for artemis	CEN_CNV_targets_b37_v1.1.0.bed	file-GFPxpJj4GVV0Pfzv4VGYf1pq