Continuing with the Nanopore Learning course on Human Genome Sequencing and Analysis, tonight I watched the video about structural variation detection. Anthony Doran, a member of the Technical Services Team with Oxford Nanopore Technologies, defined structural variation as large structural changes in your sample compared to the reference genome. The examples Doran shared on a slide included deletions, duplications, complex genomic alterations, translocations, inversions, and insertions. The structural variations are named after the type of event they represent, and Doran explained that there may be “nested” complex alterations. To detect structural variations, raw reads (fastq) are filtered, aligned to create a bam file, and filtered to create a VCF file. The variant call format (VCF) includes information about the sequence variation such as coordinates and tags/defined columns. There are tags specific for deletions, allowing a user to extract deletions from the file, for example. EPI2ME has a structural variation workflow in humans. EPI2ME Labs has a structural variant calling workflow compared to a reference that can be run locally.
