Feature Update: Visualization of Structural Variation
VCF files used for loading variation data can contain symbolic allele notations, such as <DEL>, <INS>, or <DUP>. These symbolic alleles appear in the ALT field of a VCF record and are used when the actual inserted or deleted sequence is too long or not explicitly included.
The new version of Persephone will show such structural variants (SV) in the Variants track:
In the picture above, structural variants are depicted in a dark, solid color, while the other variants (SNPs or indels) are shown in the background with semi-transparency, allowing the structural variants to stand out. The deletions are shown as green triangles pointing down. The red bars designate duplicated regions.
The SVs shown in the track can be filtered by calling the specialized form:
In this interface, we show the length distribution for different types of SV, which can also be used to filter out specific features.