Genomics short-read pipeline, release p1.1
phalaena:pipeline:PA-PL-genomics-shortread
Germline variant discovery on Illumina short-read DNA-seq. We trim with fastp, align to a reference genome (BWA-MEM2 on the CPU branch, Parabricks FQ2BAM on the GPU branch), sort and index, call variants with GATK HaplotypeCaller (or Parabricks HaplotypeCaller on GPU), annotate with SnpEff, and enrich against ClinVar. The pipeline outputs a canonical summary.json matching phalaena_backend/pipelines/SUMMARY_SCHEMA.md; the assistant reads this contract directly. Pipeline ID genomics_shortread. Source: phalaena_backend/pipelines/1.1_genomics_shortread/. API entry: phalaena_api/app/pipelines/genomics_shortread.py.
- kind
- pipeline
- status
- reviewed
- github:phalaena-automata/monorepo/phalaena_backend/pipelines/1.1_genomics_shortread
View Genomics short-read pipeline, release p1.1 on the Phalaena Wiki