Samplot

Samplot visualizes structural variants (SVs) by generating images from SV coordinates and BAM files to support visual validation through read alignments and depth signals.

Key Features:

• Multi-sample visualization: Supports visualization across multiple samples for comparative inspection of SVs.
• Sequencing technology compatibility: Handles short reads, long reads, and phased reads as input for SV visualization.
• Rapid image generation: Produces images that display read depth and sequence alignments to facilitate SV adjudication.
• Machine learning integration: Includes a trained machine learning package to reduce false positive SV calls.

Scientific Applications:

• Disease studies: Aids prioritization of potentially causal SVs by providing visual evidence of alignments and depth changes.
• Family-based analysis: Enables analysis of inherited variation within families through multi-sample visualization.
• De novo SV review: Facilitates review of de novo structural variants by highlighting supporting alignment and depth signals.

Methodology:

Takes SV coordinates and BAM files as input to produce images that highlight read alignments and depth signals and can apply a trained machine learning classifier to reduce false positives.