| 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
zhangy@sccas.cn