3 posts
A practical workflow for going from an rsID to a genotype you can trust: resolving coordinates, querying your VCF, falling back to the reads when the VCF is silent, and annotating the result correctly.
A working pipeline for taking a personal WGS VCF into R: GDS conversion, quality metrics, ancestry PCA against 1000 Genomes, variant annotation, and polygenic score computation, with the failure modes that silently corrupt each step.
A working guide to calling, normalizing, annotating, and querying SNPs from your own sequencing or array data, with the specific tools, flags, and failure modes that matter.