1。下载VarScan

参考链接：http://varscan.sourceforge.net/#install-varscan
从官网中找到VarScan的安装方式。
首先，下载.jar文件。
下载链接：https://sourceforge.net/projects/varscan/files/
我选择，VarScan.v2.3.9.jar文件。
下载之后，在文件夹下，运行：
java -jar VarScan.v2.3.9.jar

屏幕显示：
VarScan v2.3

USAGE: java -jar VarScan.jar [COMMAND] [OPTIONS]

COMMANDS:
pileup2snp Identify SNPs from a pileup file
pileup2indel Identify indels a pileup file
pileup2cns Call consensus and variants from a pileup file
mpileup2snp Identify SNPs from an mpileup file
mpileup2indel Identify indels an mpileup file
mpileup2cns Call consensus and variants from an mpileup file
somatic Call germline/somatic variants from tumor-normal pileups
copynumber Determine relative tumor copy number from tumor-normal pileups
readcounts Obtain read counts for a list of variants from a pileup file
filter Filter SNPs by coverage, frequency, p-value, etc.
somaticFilter Filter somatic variants for clusters/indels
fpfilter Apply the false-positive filter
processSomatic Isolate Germline/LOH/Somatic calls from output
copyCaller GC-adjust and process copy number changes from VarScan copynumber output
compare Compare two lists of positions/variants
limit Restrict pileup/snps/indels to ROI positions

直接使用。

2。如何使用？

链接：http://varscan.sourceforge.net/doc/index.html
后续需要的时候，会继续分析。