Software

samplot is a command line tool for rapid, multi-sample structural variant visualization. samplot takes SV coordinates and bam files and produces high-quality images that highlight any alignment and depth signals that substantiate the SV.

STIX (Structural Variant Index) supports searching every discordant paired-end and split-read alignment from thousands of sample BAMs or CRAMs for the existence of an arbitrary SV. STIX reports a per-sample count of all concurring evidence. From these counts we can, for example, conclude that an SV with high-level evidence in many samples is common and an SV with no evidence is rare.

GIGGLE is a genomics search engine that identifies and ranks the significance of shared genomic loci between query features and thousands of genome interval files. GIGGLE scales to billions of intervals, is faster (+1,000X) than existing methods, and its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEX by facilitating data integration and hypothesis generation.

LUMPY is a novel and general probabilistic SV discovery framework that naturally integrates multiple SV detection signals, including those generated from read alignments or prior evidence, and that can readily adapt to any additional source of evidence that may become available with future technological advances.

Genotype Query Tools(GQT) is command line software and a C API for indexing and querying large-scale genotype data sets like those produced by 1000 Genomes, the UK100K, and forthcoming datasets involving millions of genomes. GQT represents genotypes as compressed bitmap indices, which reduce computational burden of variant queries based on sample genotypes, phenotypes, and relationships by orders of magnitude over standard “variant-centric” indexing strategies. This index can significantly expand the capabilities of population-scale analyses by providing interactive-speed queries to data sets with millions of individuals.