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 non-commercial 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 non-commercial and commercial 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.