alterlab-nf-core-sarek

# nf-core/sarek — FASTQ-to-VCF Variant Calling The workflow-runner entry point for raw-reads-to-variants: drive the **Nextflow [nf-core/sarek](https://nf-co.re/sarek/3.8.1/) pipeline (pinned `-r 3.8.1`)** to take germline or somatic short-read FASTQ through alignment, GATK4 duplicate marking and base-quality recalibration, and SNV/indel calling, then hand the resulting VCFs to the suite's database and parsing skills for interpretation. This skill is the **command-line / workflow** counterpart to the suite's Python-library bioinformatics skills. Use it for the *raw-data-to-VCF* leg; use the library skills (`alterlab-pysam`, `alterlab-tiledbvcf`) once you hold a VCF. ## When to Use This Skill Trigger this skill when the user wants to: - Go from **FASTQ to VCF** — call variants on whole-genome (WGS) or whole-exome (WES) short reads. - Run **germline** SNV/indel calling (one or many normal samples). - Run **somatic / tumor-normal** calling (matched tumor + normal, or tumor-only). - Use **nf-core/sarek** specifically, or want a reproducible "GATK best-practices alignment-to-VCF" pipeline without hand-writing every step. - Resume a run from an intermediate **`--step`** (already have BAM/CRAM, only need recalibration or variant calling). ### Does NOT Trigger — route adjacent requests here | The request is really about… | Route to | |---|---| | Parsing / filtering / reading an **existing** VCF/BAM in Python (pysam/htslib) | `alterlab-pysam` | | **Storing / querying** lar...