Introduction

We developed VariantBam, a C ++ read filtering and profiling tool for use with BAM, CRAM and SAM sequencing files. VariantBam provides a flexible framework for extracting sequencing reads or read-pairs that satisfy combinations of rules, defined by any number of genomic intervals or variant sites. We have implemented filters based on alignment data, sequence motifs, regional coverage and base quality. For example, VariantBam achieved a median size reduction ratio of 3.1:1 when applied to 10 lung cancer whole genome BAMs by removing large tags and selecting for only high-quality variant-supporting reads and reads matching a large dictionary of sequence motifs. Thus VariantBam enables efficient storage of sequencing data while preserving the most relevant information for downstream analysis.VariantBam and full documentation are available at github.com/jwalabroad/VariantBamrameen@broadinstitute.orgSupplementary data are available at Bioinformatics online.

Publications

  1. VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.
    Cite this
    Wala J, Zhang CZ, Meyerson M, Beroukhim R, 2016-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Jeremiah Wala
    Developer

    The Broad Institute of Harvard and MIT, Cambridge, United States of America

  2. Cheng-Zhong Zhang
    Developer

    The Broad Institute of Harvard and MIT, Cambridge, United States of America

  3. Matthew Meyerson
    Developer

    The Broad Institute of Harvard and MIT, Cambridge, United States of America

  4. Rameen Beroukhim
    Investigator

    The Broad Institute of Harvard and MIT, Cambridge, United States of America

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Summary
AccessionBT005697
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByRameen Beroukhim