Workflow Description
using varscan to call somatic variants
Macros Interface
Macro Name Description
SAMTOOLS path of samtools
REF path of reference genome
NORMAL_BAM path of normal bam
TUMOR_BAM path of tumor bam
VARSCAN path of varscan.jar
VARSCAN_PROCESS_SOMATIC_SNP_PARAMS varscan processSomatic params for snp
VARSCAN_PROCESS_SOMATIC_INDEL_PARAMS varscan processSomatic params for indel
SAMPLE_NAME sample name
BAM_READCOUNT path of bam-readcount
BAM_READCOUNT_PARAMS bam-readcount params
VARSCAN_FPFILTER_PARAMS varscan fpfilter params


Zhang Yu