Reference

Last updated on 2026-09-04 | Edit this page

Reference

Introduction to IGV

  • IGV is a free desktop genome browser that runs locally and supports many file formats (FASTA, BED, BAM, TDF, VCF, and more).

IGV Basics

  • File > Load from Server… loads example data hosted by the IGV team.
  • Zoom levels: whole genome (All) → chromosome → region → base pair.
  • Click-and-drag on the ruler to zoom into a region; double-click a track to zoom to a point (Alt-click to zoom out).
  • Type a locus or gene name into the search box and click Go to jump directly to it.
  • Right-click a gene track for Collapsed / Expanded / Squished display modes.
  • Genomes > More… adds other IGV-hosted genomes to the drop-down menu.
  • Tools > Combine Data Tracks adds, subtracts, multiplies, or divides two numeric tracks into a new derived track.

Loading Your Own Genome

  • Genomes > Load Genome from File… loads a reference sequence (FASTA).
  • File > Load from File… loads any other local track (e.g. a BED annotation file).
  • A genome loaded from a bare FASTA has no gene names or cytoband ideogram until you add annotation tracks yourself.

Viewing Alignments and SNPs

  • IGV finds a BAM’s .bai index automatically if it is named correctly and kept alongside the BAM file — never load the .bai directly.
  • Right-click aligned reads for Sort alignments by (e.g. base, read strand) and Color alignments by (e.g. read strand) options.
  • Warning signs of a false-positive variant: low base quality (shaded mismatches), a mismatch confined to one strand in a non-strand-specific library, and (via BLAT) many equally-good alternative alignments elsewhere.
  • Tools > BLAT…, or right-click a read and choose BLAT read sequence, checks whether a read/feature aligns uniquely.

Precomputing Coverage with igvtools

  • Tools > Run igvtools… > Count precomputes a .tdf coverage summary for a BAM file.
  • Right-click a coverage track and select Load pre-computed coverage data… to attach a .tdf file.

Viewing RNA-seq Data

  • View > Preferences > Alignments > Splice Junction Track enables junction arcs for RNA-seq BAM tracks.
  • Right-click a junction/alignment track and select Sashimi Plot for a combined coverage + junction view; Set Junction Coverage Min filters out low-count junctions.

Viewing Variants and Genotypes

  • A VCF track has a variant sites panel and a per-sample genotypes panel.
  • Variant sites: blue = reference allele, red = alternate allele. Genotypes: grey = homozygous reference, blue = heterozygous, cyan = homozygous alternate.
  • Sample metadata comes from an auxiliary tab-delimited file (header row of attribute names, first column of sample names matching the VCF).
  • Search using gene:protein-change (e.g. APOL1:S342G) as well as by coordinate or gene name.
  • Right-click genotypes for Group By… (a sample attribute, e.g. population), Display Mode, Color By, and sort options.

Viewing Structural Variants

  • A larger-than-expected inferred insert size (colored red) indicates a deletion; a coverage drop appears between the two breakpoints.
  • Reads colored by an unexpected mate chromosome indicate an inter-chromosomal fusion.
  • Same-strand (forward-forward or reverse-reverse) discordant pairs indicate an inversion; right-click alignments and select View as pairs to see pair relationships clearly.

Viewing Long-Read Sequencing Data

  • View > Preferences > Alignments: indel hiding thresholds and Quick consensus mode filter raw long-read errors so consensus signal is easier to see.
  • MAPQ (0–255) reflects alignment confidence; low MAPQ is a warning sign for any variant called from that read.
  • A single long read can reveal a structural variant directly by splitting across its breakpoint.
  • File > Load from URL… streams a remote BAM/CRAM without downloading it first; right-click Link supplementary alignments plus Color alignments by > Read strand (pink = forward, purple = reverse) reveals an inversion within single linked reads.
  • Color/group reads by HP (haplotype) tag (Color/Group alignments by > Tag, tag name HP) to separate two phased alleles for comparison, or to tell a heterozygous structural variant (one haplotype) from a homozygous one (both).

Glossary

BAM
Binary Alignment/Map format; stores aligned sequencing reads. Requires a .bai index file for random access.
BED
A simple tab-delimited format for genomic intervals/features.
BLAT
An alignment search tool used in IGV to check whether a read or feature sequence aligns uniquely, or almost as well to other locations.
CIGAR string
A compact code in a SAM/BAM record describing how a read’s bases align against the reference (matches, insertions, deletions).
Coverage
The number of aligned reads overlapping each position in the genome.
Cytoband
A stained-banding pattern used to represent chromosome structure at low zoom levels.
FASTA
A plain-text format for nucleotide or protein sequences.
Genotype
The specific allele(s) an individual sample carries at a variant site.
Haplotype tag (HP)
A BAM tag assigned by a phasing tool (e.g. WhatsHap, LongPhase) that labels which parental haplotype a read belongs to.
Insert size
The distance spanned by a paired-end fragment, from the outer edge of one read to the outer edge of its mate.
Inversion
A structural variant in which a segment of the genome is reversed in orientation between two breakpoints.
Mapping quality
A score reflecting how confident an aligner is that a read is placed at the correct genomic location.
Reference genome
The assembled genome sequence that reads, genes, and variants are positioned against.
Sashimi plot
An IGV visualization combining exon coverage and splice-junction reads for RNA-seq data.
Split read
A single sequencing read whose parts align to two different locations (or orientations) in the reference, often evidence of a structural variant breakpoint.
Splice junction
The point where two exons are joined together after intron removal; represented in IGV as an arc connecting the two exons.
TDF
A binary, indexed summary format used by IGV to store precomputed coverage/summary data at multiple resolutions.
Track
A single row (or set of rows) of data displayed in IGV, such as a gene annotation track, an alignment track, or a variant track.
VCF
Variant Call Format; stores variant calls and, optionally, per-sample genotypes.