| Macro Name | Description |
|---|---|
| R1 | r1 end of paired fastq file |
| R2 | r2 end of paired fastq file |
| SAMPLE_NAME | sample name |
| ID | sample id |
| LIBRARY | sample library |
| PLATFORM | sequencing platform,eg.Ilumina |
| BWA | path of bwa bin |
| SAMTOOLS | path of samtools bin |
| GATK4 | path of gatk4 bin(gatk) |
| REF | path of reference genome |
| GATK4_BASERECALIBRATE_PARAMS | gatk4 BaseRecalibrator params |
| PICARD | path of picard jar |
| THREAD | bwa thread |
| TMP | tmp directory (need enough disk space to write cache file) |
Zhang Yu
zhangy@sccas.cn