alterlab-nf-core-sarek

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.