FASTQ, BAM, VCF — what they are

Three file formats sit at different points in the pipeline:

FASTQ — raw sequencing reads, each with a nucleotide sequence and per-base
  quality scores. Largest and most sensitive; you do not retrieve over this.
BAM (binary SAM) — reads aligned to reference coordinates; intermediate,
  used for variant calling and visualization (IGV).
VCF (Variant Call Format) — a text table of positions where the sample
  differs from the reference — chromosome, position, reference allele,
  alternate allele, genotype, quality, and an INFO field full of annotations.

The VCF (and the report built from it) is the natural retrieval target: it's compact, structured, and clinically meaningful.