What is a VCF file and what is it used for?

The VCF (Variant Call Format) file is the result of processing your data in FASTQ format. This file compares your raw DNA with a “reference genome” (a standard human model). The VCF file lists the locations where your DNA differs from the reference genome, meaning the variants (SNPs, insertions, or deletions) found in your genetics.

VCF files are usually compressed in .vcf.gz format. Bioinformatics tools are designed to read these compressed files directly, although they can also be decompressed using tools like 7zip or gzip.

Who is it useful for?

• Curious users: If you want to search for a specific genetic mutation (for example, at chromosome position 14, 64877827 in the MTHFD1 gene).
• Third-party analysis: This format is the required standard if you wish to upload your data to other services that accept WGS data to obtain information on ancestry or health.

Strengths

• Actionable: This file contains the actual genetic data.
• Compact: By listing only the differences, it is much smaller than the raw FASTQ files.

Limitations

• Processed data: The file depends on the current reference genome used by tellmeGen (GRCh37). If the reference model changes, this file will become outdated, unlike the FASTQ file.

How to open and use the file

• Basic use: After decompressing it, it can be opened as a text file (with Notepad++ on Windows, TextMate on Mac).
• Advanced use: Use a VCF viewer or the Integrative Genomics Viewer (IGV) to see the variants visually. You can also use third-party tools like Galaxy to perform operations with your VCF file.

System requirements

• Operating system: Windows, Mac, or Linux.
• RAM: 8GB standard.
• Storage: <1GB.