Automated Bash pipeline for variant analysis in family trio. From raw FASTQ to VCFs. Supports Mendelian inheritance models (AR, de novo, AD) using Bowtie2, FreeBayes, Bedtools and BCFtools. Includes integrated QC reports (FastQC, Qualimap, MultiQC).

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Pipeline for automated genomic variant analysis in inherited diseases, integrating alignment, variant calling, and quality control