(current) A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

Publicly available statistical genetics data and analysis. 1000G, HGDP, SGDP, and GIAB. Reproducible global ADMIXTURE with variable K.

GATK4 germline variant calling (Nextflow DSL2): BWA-MEM -> MarkDuplicates -> BQSR -> HaplotypeCaller -> hard-filter, benchmarked against a GIAB truth set (precision/recall/F1).

Production Nextflow DSL2 germline variant calling pipeline with biomarker reproducibility analysis and AWS execution

Variant calling benchmarking on GIAB HG002 (WES chr22) using hap.py; SNP/INDEL Precision/Recall/F1.

Benchmark asking whether a variant caller's confidence is honest, not just accurate — GIAB-scored performance stratified by genomic difficulty, QUAL calibration, and quality filtering treated as an abstention decision