Variant tracks

Visualizing variant tracks from the VCF format alongside the original alignment evidence track is a common workflow for validating your results, shown below:

Variant track indicating a SNP alongside the alignment track evidence.

Variant widget

The variant features have a specialized widget that contains a table indicating all the calls that were made in a multi-sample VCF. Some VCF files, like the 1000 genomes VCF, can contain thousands of samples in a single file. This table can display the details.

Screenshot showing the variant feature sidebar with a filtered by genotype (with alternative allele '1'). Users can also filter by sample name or other attributes.

Live demo — example showing a deletion in a trio

We can use the Variant widget to sort by samples that have the genotype (e.g. GT being non-zero, zero is the REF allele, any non-zero value is one of the ALT alleles)

Multi-sample variant matrix display

The matrix display shows multi-sample VCFs as a dense heatmap where each row is a sample and each column is a variant position. This makes genotype patterns — shared variants, population structure, runs of homozygosity — visible at a glance in ways that a per-position track cannot.

Example screenshot of looking at a deletion structural variant, with alignment evidence from a mom, dad, and child (trio). The first two samples (mother, child) have complete (homozygous) deletion in this region, while the father has a heterozygous deletion. The blue markers show 'soft clipping' at the boundaries of the deletion. The right panel shows all the samples, sorted by their genotype