What it does

Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.

For more information on local realignment around indels using the GATK, see this tool specific page.

To learn about best practices for variant detection using GATK, see this overview.

If you encounter errors, please view the GATK FAQ.

Inputs

GenomeAnalysisTK: RealignerTargetCreator accepts an aligned BAM input file.

Outputs

The output is in GATK Interval format.

Go here for details on GATK file formats.

Settings:

windowSize          window size for calculating entropy or SNP clusters
mismatchFraction    fraction of base qualities needing to mismatch for a position to have high entropy; to disable set to <= 0 or > 1
minReadsAtLocus     minimum reads at a locus to enable using the entropy calculation
maxIntervalSize     maximum interval size

Citation

For the underlying tool, please cite DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8.

If you use this tool in Galaxy, please cite Blankenberg D, et al. In preparation.