Calls germline variants from BAM files using GATK HaplotypeCaller in GVCF mode. Supports multiple samples in parallel, producing per-sample g.VCF files ready for joint genotyping.

Single-cell RNA-seq downstream analysis pipeline: preprocessing (normalize, log-transform, HVG selection, scaling, PCA), Leiden clustering, and UMAP visualization. Outputs processed h5ad, UMAP PNG, and cluster assignment CSV.