Variant Calling & Genomic File Formats

The FASTQ-to-VCF pipeline — how raw reads become a filtered list of called variants, and the file formats each stage produces.

Read

50 min

Practice MCQs

25

Interview QA

25

Edition

v4

Editorial status

Reviewed

Relevant for

Computational Biologist

Scope: VCF 4.5 / BCF 2.2, SAM/BAM and CRAM 3.1 specifications; current GATK, bcftools, samtools, GIAB, vcfeval and GA4GH VRS guidance reviewed 2026-09-04.