alterlab-nf-core-sarek

name	alterlab-nf-core-sarek
description	Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.8.1 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR against the GATK GRCh38 resource bundle (dbSNP, Mills/1000G indels), and selects callers — explicitly correcting that sarek defaults to Strelka when --tools is unset (pass haplotypecaller for GATK best practice or deepvariant for CNN accuracy), with a non-Nextflow manual GATK4 fallback. Use when the user wants a variant-calling pipeline, FASTQ to VCF, germline or somatic SNV/indel calling, nf-core/sarek, GATK best-practices alignment-to-VCF, or BQSR/HaplotypeCaller/Mutect2/DeepVariant; annotate hits with alterlab-clinvar/alterlab-gnomad/alterlab-cosmic, parse VCFs with alterlab-pysam, store at scale with alterlab-tiledbvcf. Part of the AlterLab Academic Skills suite.
license	MIT
allowed-tools	Read Write Edit Bash(python:*) Bash(uv:*) Bash(nextflow:*)
compatibility	Requires Nextflow plus a container engine (Docker/Singularity/Apptainer) or conda; the pipeline pulls nf-core/sarek 3.8.1 and reference bundles over the network on first run. The manual GATK4 fallback needs bwa-mem2 + samtools + gatk4 (bioconda) and runs offline once references are local. No API key. Indexing, BQSR and variant calling are long, compute-heavy jobs — good candidates to run locally rather than through repeated API calls.
metadata	{"skill-author":"AlterLab","version":"1.0.0","last_updated":"2026-06-06"}

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:

• 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 large multi-sample variant stores (TileDB-VCF arrays)	alterlab-tiledbvcf
Clinical significance of a called variant (pathogenic/benign)	alterlab-clinvar
Population allele frequencies for a called variant	alterlab-gnomad
Somatic mutation catalogue / cancer census lookup	alterlab-cosmic
RNA-seq transcript/gene quantification (salmon/kallisto), not DNA variants	alterlab-rnaseq-quant
16S/ITS FASTQ → feature table