Genomics Data Processing

Genomics data processing is the pipeline from raw DNA sequencer output (millions of short reads) to variant calls (mutations identified). Key steps: (1) quality control (discard low-quality reads), (2) alignment (map reads to reference genome using BWA), (3) realignment and base quality recalibration, (4) variant calling (GATK HaplotypeCaller), (5) annotation (interpret variants with databases like ClinVar, dbSNP). Output is a VCF (Variant Call Format) file listing all variants with quality scores. Downstream analysis identifies disease-causing mutations, performs population genetics, or screens for predisposition genes.