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 bam2pindel.pl) 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.

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.

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.

RefCov v0.3 provides critical fixes and several new features. Fixes include restoring several modules that were absent in the previous release. New features include: 1) cluster-coverage for detecting contiguous clusters of sequence reads across a reference, 2) the ability to evaluate coverage of entire chromosomes using the BAM file header as the region-of-interest, ex. --roi-file-path=$BAM --roi-file-format=bam, 3) normalization of coverage using a defined Perl-compatible equation, 4) relative coverage based on a defined list of size bins, and 5) optional output of the chromosome start and end as BED-style columns.

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MuSiC (Mutational Significance in Cancer) 0.3 is now available for download featuring numerous fixes and several new features. MuSiC performs a variety of statistical analyses on the somatic (and germline) alterations discovered in any cancer cohort. Improvements in this version include an enhanced significantly mutated gene test which introduces the ability to 1) take into account sample-specific mutation rates and 2) identify significantly mutated non-genic regions of the genome. The clinical correlation module now features a generalized linear model option allowing for the elimination of covariate influences on mutation-phenotype relationships. Support for MAF 2.2 and for Pfam annotation of GRCh37 (hg19) are now standard. Additionally, several MuSiC components have been optimized and parallelized for faster execution.

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