软件相关资源信息

软件文献
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
Daniel
Software implementation
软件获取
varscan.sourceforge
varscan.github
The VarScan 2 core software was developed in Java; the false-positive filter was implemented in Perl. Binary executables, scripts, and source code are free for noncommercial use and available at http://varscan.sourceforge.net.
The false-positive filter requires the bam-readcount utility (D. Larson et al., https://github.com/genome/bam-readcount), which is written and compiled in C.

Varscan的使用

samtools mpileup -f ref.fasta sample.bam |
java -jar VarScan.v2.3.3.jar mpileup2indel
–output-vcf 1
–vcf-sample-list sample_names.list

sample.varscan.vcf