java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I input.bam --known indels.vcf -o forIndelRealigner.intervals
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Inputs | |||
| --known | [] | Input VCF file with known indels | |
| Optional Outputs | |||
| --out  -o | NA | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --maxIntervalSize  -maxInterval | 500 | maximum interval size; any intervals larger than this value will be dropped | |
| --minReadsAtLocus  -minReads | 4 | minimum reads at a locus to enable using the entropy calculation | |
| --mismatchFraction  -mismatch | 0.0 | fraction of base qualities needing to mismatch for a position to have high entropy | |
| --windowSize  -window | 10 | window size for calculating entropy or SNP clusters | |