Analysis of the raw sequence data requires bioinformatics expertise and software.
For annotation and analysis of sequence variants in the VCF file there are several commercial and noncommercial tools available. Commonly used and freely available command line tools include:
- VEP (https://www.ensembl.org/info/docs/tools/vep/index.html)
- ANNOVAR (http://annovar.openbioinformatics.org/en/latest/)
- SnpEff (http://snpeff.sourceforge.net)
There are also several commercial and noncommercial web browser-based or stand-alone software for variant annotation and analysis. For sequence read analysis, GATK is one of the most commonly used toolkits https://software.broadinstitute.org/gatk/.
To visualize the content of VCF or BAM files in genomic context the Integrative Genome Browser (IGV) can be used, both as a stand-alone application and a web-browser interface.