A VCF (Variant Call Format) file is produced by processing your sequencing data and comparing it with the GRCh37 reference genome. It lists the positions where your DNA differs from the reference: single-letter variants (including SNPs), insertions and deletions.
- What it is used for: searching for a specific variant or uploading your data to third-party services that accept sequencing files.
- Advantages: it contains your actual variants and, because it only lists differences, it takes up much less space than a FASTQ file.
- Limitation: its positions refer to the GRCh37 reference genome; to use a more recent reference, such as GRCh38, the coordinates must be converted or the file regenerated from the FASTQ data.
It downloads as a compressed file (.vcf.gz). You can decompress it with 7-Zip or gzip and open it as text, or view it graphically with IGV or tools such as Galaxy. It works on Windows, macOS or Linux, with 8 GB of RAM. The compressed file is a few hundred megabytes, but it can exceed 1 GB when decompressed, so you will need an editor capable of handling large files to open it as text.