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 |