| 27 | | * Map reads to reference after QC'ing |
| 28 | | * Mark duplicates: sequencing errors can propagate due to amplification (use Picard Tools) |
| 29 | | * Indel-based realignment: misalignment by aligner is likely to occur near indels (use RealignerTargetCreator and IndelRealigner) |
| 30 | | * Base quality recalibration: base quality score will be made more accurate (use BaseRecalibrator and PrintReads) |
| 31 | | * Run UnifiedGenotyper to call variants |
| | 27 | * See [wiki:SOPs/variant_calling_GATK Using GATK to call variants from short-read sequencing]. |
