egg_generate_rd_wgs_workbook (DNAnexus Platform App)

What does this app do?

Generates an Excel workbook from a Genomics England rare disease case JSON.

What data are required for this app to run?

Packages

• Python packages (specified in requirements.txt)

Inputs Required

• json: a GEL RD WGS JSON with data to be put into a workbook
• refseq_tsv: a RefSeq TSV with Ensembl protein and transcript IDs
• mane_file: a MANE summary.txt.gz summary file
• config: config file with DNAnexus file IDs for HPO obo files, and thresholds for de novo quality score for SNVs and CNVs

Optional

• acmg: number of SNV ACMG interpretation sheets to add to the workbook
• cnv: number of CNV interpretation sheets to add to the workbook
• epic_clarity: .xlsx file of Epic Clarity export, will be used to add sample IDs to the workbook

What variants are displayed in the workbook?

GEL Tiering sheet

• TIER1 SNVs
• TIER2 SNVs
• TIERA/TIER1 CNVs
• TIER1 STRs Extended analysis sheet
• Exomiser Top 3 ranked variants
  • only displayed if:
    • score >= 0.75
    • variant is not mitochondrial and untiered.
    • variant has not already been reported in GEL tiering sheet.
• De novo variants:
  • all variants with a de novo score above the threshold, regardless of tier.

What does this app output?

This app outputs an Excel workbook