ngs-cli-toolkit

The core command-line NGS workhorses for going from raw reads to variants — bwa-mem2/minimap2/bowtie2 (alignment), samtools (BAM sort/index/stats/view), bcftools (VCF call/filter/normalize/query), GATK4 (BQSR, HaplotypeCaller, best practices), and plink2 (genotype QC, PCA, GWAS). Use for read alignment, BAM/CRAM manipulation, variant calling and VCF wrangli…

Independent GitHub snapshot · Automated classification · Original documentation governs