Varscan2 Call snp_indel

Varscan2官方文档

01:mpileup文件准备
samtools mpileup -d 1000 -Q 20 -q 30 -f /data2/references/Homo_sapiens/hg38.genomic.fa pa01_tumor1.bam >pa01_tumor1.mpileup 

02:使用Varscan2的 somatic 命令
USAGE: java -jar VarScan.jar somatic [normal_pileup] [tumor_pileup] [output] 
OPTIONS
        normal_pileup - The SAMtools pileup file for Normal
        tumor_pileup - The SAMtools pileup file for Tumor
        output - Output base name for SNP and indel output

03:somatic 命令 可选参数
OPTIONS:
	--output-snp - Output file for SNP calls [default: output.snp]
	--output-indel - Output file for indel calls [default: output.indel]
	--min-coverage - Minimum coverage in normal and tumor to call variant [8]
	--min-coverage-normal - Minimum coverage in normal to call somatic [8]
	--min-coverage-tumor - Minimum coverage in tumor to call somatic [6]
	--min-var