java -jar GenomeAnalysisTK.jar -T SimulateReadsForVariants -R reference.fasta -V input_variants.vcf -o simulated_reads.bam --readDepth 50 --errorRate 25
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --variant  -V | NA | Input VCF file | |
| Required Outputs | |||
| --out  -o | NA | Reads corresponding to variants | |
| Optional Parameters | |||
| --errorRate  -ER | 20 | Base error rate (Phred-scaled) | |
| --readDepth  -DP | 20 | Read depth to generate | |
| --readLength  -RL | 101 | Read lengths (bp) | |
| Advanced Parameters | |||
| --readSamplingMode  -RSM | CONSTANT | Sampling mode | |
| --rgPlatform  -RGPL | ILLUMINA | Sequencing platform | |