VCF track

Supported variant files

The browser view can load variant calls from:

  • VCF

  • compressed VCF such as .vcf.gz, .vcf.xz, and .vcf.zst

When one or more VCF files are loaded, seqhiker shows a shared VCF track.

Layout

The VCF track shows:

  • one row per sample

  • all loaded VCF files combined into the same track

  • empty rows except at variant sites

For now, the track renders:

  • SNPs

  • insertions

  • deletions

  • complex replacement variants

Rendering

SNPs are shown as coloured blocks with genotype text when there is enough room.

Genotype colours are grouped into three classes:

  • reference call (0/0)

  • heterozygous call (0/1, 1/2, 1/3, and similar)

  • homozygous ALT call (1/1)

For heterozygous SNPs, the text shows both alleles, for example:

  • A/G

  • G/T

For homozygous calls, the text shows only the called allele.

Deletions and insertions use compact glyphs similar to the read track. Complex replacement variants use a wave-like glyph.

Interaction

You can:

  • click a variant to select it

  • if the right-hand panel is already open, clicking a variant updates it

  • double-click a variant to open its details in the right-hand panel

The right-hand panel shows:

  • sample

  • file

  • type

  • CHROM / POS / ID

  • REF / ALT / QUAL / FILTER / INFO

  • genotype fields for the selected sample