MendelScan v1.1.1

This is the initial release of MendelScan, a software package for analyzing variants identified by family-based sequencing of rare genetic diseases. There are three main functions included with this release:

  • score -- prioritize variants in a VCF based upon segregation, annotation, population frequency, and gene expression
  • rhro -- apply rare heterozygote rule out to map dominant disease genes
  • sibd -- apply shared IBD analysis to map disease genes

A manuscript describing this tool has been submitted; in the interim, please cite MendelScan by noting the version number and citing its home URL:

Introducing DGIdb

In the era of high throughput genomics, investigators are frequently presented with lists of mutated or otherwise altered genes implicated in disease. Numerous resources exist to help form hypotheses about how such genomic events might be targeted therapeutically or prioritized for drug development. However, utilizing these resources typically requires tedious manual review of literature and knowledge bases. No informatics tools currently exist which mine these resources and provide a simple interface for searching lists of genes against the existing compendia of both known or predicted drug-gene interactions and potentially druggable genes. The Drug-Gene Interaction database (DGIdb) addresses this challenge. Drug-gene interactions have been mined from existing databases and literature to populate DGIdb. Similarly, genes have been categorized as potentially druggable according to membership in selected pathways, molecular functions and gene families. Currently, DGIdb contains 2,611 genes and 6,307 drugs involved in 14,144 drug-gene interactions, and 6,761 genes that belong to one or more of 39 potentially druggable gene categories. Users can enter a gene or list of genes to retrieve all known or potentially druggable genes in that list. Results can be filtered by source, interaction type, or treatment type and are sorted by source trust level. Our goal was to create a user-friendly search tool and comprehensive database of genes that have the potential to be druggable with a particular focus on cancer. DGIdb can be accessed programmatically or through a web-based interface at

Pindel 0.2.4 Available

An updated version of Pindel is available for download.

Pindel is a program that detects short indels and complex structural variants (large deletions, inversions, tandem duplications, mobile element insertions and translocations) from next-generation sequence data using pattern growth.

It takes either extracted reads (using sam2pindel or or multiple bam files as input. A pindel2vcf converter is provided to report variant calls in VCF format.

The source code for Pindel is available on GitHub, and pre-built packages for Ubuntu 10.04 systems are available from The Genome Institute. For installation instructions, see the Pindel project page.

iBWA Alpha v0.5 Released

Source code and Ubuntu 10.04 (64-bit) packages of iBWA Alpha v0.5 are now available for testing. iBWA is a fork of Heng Li's BWA aligner with support for iteratively adding alternate haplotypes, reference patches, and variant hypotheses. This enables you to leverage existing tools and pipelines in the diverse BWA ecosystem while also creating new analysis opportunities.

  • Take advantage of improvements to the human reference made available by the Genome Reference Consortium.
  • Represent alternate alignments in the context of the primary human reference.

For additional information about BWA please see Heng Li's BWA @ SourceForge or BWA's manual page.

Genome MuSiC v0.4 Released

MuSiC v0.4 is now available for download. This release adds new visualization tools, performance improvements, support for TCGA MAF v2.3, and coverage files in UCSC WIG format when BAMs are impractical. Here is a complete changelog:

  • Added tools to generate typical visualizations like Kaplan-Meier survival estimates, and mutation status matrices.
  • Support for TCGA Mutation Annotation Format (MAF) version 2.3.
  • Performance improvements in mutation rate calculations, and more efficient memory usage.
  • Added support for wiggle track format files describing coverage, if BAMs are unavailable.