nf-core/sarek — FASTQ-to-VCF Variant Calling

The workflow-runner entry point for raw-reads-to-variants: drive the Nextflow nf-core/sarek 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: