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VarScan:variant detection in massively parallel sequencing data  

2012-03-05 15:17:37|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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       VarScan是一个基于Java的工具,用于识别个体和群体样本的SNP和INDELS检测。

Installing VarScan

The new release (VarScan 2) is written in Java and thus runs on any operating system (Linux, UNIX, Mac OSX, even Windows) through the Java Virtual Machine. To install it, you must download the VarScan JAR file from SourceForge. Then, run VarScan from the command line:

java -jar VarScan.v2.2.jar

Usage information will be displayed. For details on using VarScan, please see the User's Manual.

Citing VarScan

Please note the version number, and cite the publications below with URL to cite VarScan:

VarScan 1: Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID: 19542151
VarScan 2: Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., & Wilson, R. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111
URL: http://varscan.sourceforge.net

License

VarScan is free for non-commercial use. For details on commercial licensing or general questions, please contact dkoboldt (at) genome (dot) wustl (dot) edu.

Release Notes

02-29-2012     Happy Leap Day: User's manual and documentation updated to cover mpileup/multi-sample calling, somatic CNA detetion, and other items.
02-03-2012     VarScan 2 published in Genome Research with demonstration of somatic mutation and copy number alteration calling.
10-14-2011     VarScan v2.2.8 released with new somatic calling features: Tumor-normal mpileup compatibility and VCF 4.1 output option.
08-16-2011     VarScan v2.2.7 released with copyCaller post-processing, mpileup compatibility for multiple-sample calling, and VCF 4.0 output option.
07-29-2011     New VarScan copynumber function for identifying copy number changes in tumor-normal exome pairs. See the copy number calling section for details.
04-29-2011     New Support FAQ launched! Find answers to frequently-asked questions about VarScan usage, parameters, input/output, and other topics.
04-28-2011     VarScan v2.2.5 released! New features include normal and tumor purity input parameters for somatic mutation calling, which can improve sensitivity for genomes with reduced tumor cellularity, or matched normal samples that contain some tumor cells (e.g. leukemias).
Download site:http://sourceforge.net/projects/varscan/files/
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