alterlab-nf-core-sarek
De la autor
Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.10.0 — 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.
Instalare
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-nf-core-sarek -a claude-code
Se instalează în .claude/skills/alterlab-nf-core-sarek/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
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De ce 77
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Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- gatk-variant-callingjaechang-hits/SciAgent-SkillsGATK Best Practices for germline SNP/indel calling from WGS/WES BAMs. Per-sample HaplotypeCaller GVCFs, GenomicsDBImport, GenotypeGVCFs joint calling, VQSR or hard filters. Requires BWA-MEM2-aligned, markdup, BQSR BAMs. Use DeepVariant for a faster DL alternative; GATK is the NIH/ENCODE standard.Știință★ 385
- alterlab-scanpyAlterLab-IEU/AlterLab-Academic-SkillsRun the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data through clustering, cell-type annotation, DE, or pseudotime workflows; for building or reading the .h5ad data structure itself (layers, obs/var, concatenation, backed mode) prefer alterlab-anndata instead, and for RNA velocity from spliced/unspliced counts prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.Altele★ 84
- alterlab-phylogeneticsAlterLab-IEU/AlterLab-Academic-SkillsBuild phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstructing trees from sequences (FASTA) for evolutionary analysis, microbial genomics, viral phylodynamics, protein-family studies, or molecular-clock dating. For manipulating/comparing an EXISTING Newick tree (prune, root, Robinson-Foulds, duplication/speciation events) use alterlab-etetoolkit; for plain sequence parsing/translation use alterlab-biopython. Part of the AlterLab Academic Skills suite.Știință★ 84
- variant-callingawslabs/hcls-agent-skillsGermline and somatic short-variant calling pipeline for Illumina short-read data. Use when the user mentions BWA, BWA-MEM2, GATK, HaplotypeCaller, Mutect2, VCF, GVCF, VQSR, variant calling, germline, somatic, SNV, or indel calling from FASTQ/BAM.Altele★ 71
- alterlab-tiledbvcfAlterLab-IEU/AlterLab-Academic-SkillsStore and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays, add samples incrementally, run fast parallel region/sample queries, and export back to VCF. Use when managing population-genomics variant datasets that are too large for flat VCF, building joint variant stores, or querying thousands of samples by region. Part of the AlterLab Academic Skills suite.Știință★ 84
- alterlab-clinvarAlterLab-IEU/AlterLab-Academic-SkillsQuery NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assessing whether a variant is pathogenic, likely pathogenic, VUS, likely benign, or benign, resolving conflicting interpretations, or annotating a VCF with ClinVar clinical significance. For population allele frequencies by ancestry use alterlab-gnomad; for somatic cancer mutation frequencies use alterlab-cosmic. Part of the AlterLab Academic Skills suite.Știință★ 84
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