Initial commit: digital-patients pipeline (clean, no large files)

Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
2026-03-26 15:15:23 +01:00
commit 9e6a16c19b
45 changed files with 7207 additions and 0 deletions
--- a/app_filter/README.md
+++ b/app_filter/README.md
@@ -0,0 +1,5 @@
+Run command
+
+```
+vep --config vep.ini -i ${input_vcf} -o ${input_vcf.simpleName}_cosmic.vcf
+```