Repository for code related to small tasks for supporting the RD service.
| Ticket | Summary |
|---|---|
| EBH-3338 | Pull out a list of medicover samples for which we do not have medicover results JSONs in DNAnexus |
| EBH-3050 | Determine how many workbooks were released/not released (based on number of variants filtered) per clinical indication since new filtering introduced |
| DI-773 | Gather and plot QC metrics |
| DI-1057 | Validate East GLH RD Test Directory hosted on AWS RDS |
| DI-1094 | CEN/WES GRCh38 egg_sex_check thresholds - August 2024 |
| DI-1189 | Create new PanelApp JSON file |
| DI-435 | Find and merge VCFs for creation of a GRCh38 POP AF VCF |
| DI-1294 | Remove any content from the PID fields in workbooks in a given path |
| DI-1299 | Compare values between GRCh37 and GRCh38 for Somalier |
| DI-1141 | Compare Consequence, HGVSc, and HGVSp values between VEP versions and compare with output batch of VariantValidator |
| DI-1466 | Script to download dias files |
| DI-1480 | Script to compare filtered variants for the same samples |
| EBH-4325 | Script to clone QC passing TWE VCFs from 002s to specific 003 project |
| EBH-4350 | Script to find all GRCh38 CEN and TWE VCFs, unarchive if necessary, and write the file IDs to file |
| DI-2556 | Script to add headers to static panel beds, that details the version and genome assembly. These static beds will be fetched by eggd_dias_batch to be used in eggd_vep, eggd_athena and eggd_annotate_excluded_regions |
| EBH-4581 | Script to extract SpliceAI score and GTEX data for certain variants and genes |