What it does

DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score.

For more information on the GATK Depth of Coverage, 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: DepthOfCoverage accepts aligned BAM input files.

Outputs

The output is in various table formats.

Go here for details on GATK file formats.

Settings:

calculateCoverageOverGenes     File     NA     Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
ignoreDeletionSites     boolean     false     Ignore sites consisting only of deletions
includeDeletions     boolean     false     Include information on deletions
maxBaseQuality     byte     127     Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
maxMappingQuality     int     2147483647     Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
minBaseQuality     byte     -1     Minimum quality of bases to count towards depth. Defaults to -1.
minMappingQuality     int     -1     Minimum mapping quality of reads to count towards depth. Defaults to -1.
nBins     int     499     Number of bins to use for granular binning
omitDepthOutputAtEachBase     boolean     false     Will omit the output of the depth of coverage at each base, which should result in speedup
omitIntervalStatistics     boolean     false     Will omit the per-interval statistics section, which should result in speedup
omitLocusTable     boolean     false     Will not calculate the per-sample per-depth counts of loci, which should result in speedup
omitPerSampleStats     boolean     false     Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
outputFormat     String     rtable     the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
partitionType     Set[Partition]     [sample]     Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
printBaseCounts     boolean     false     Will add base counts to per-locus output.
printBinEndpointsAndExit     boolean     false     Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
start     int     1     Starting (left endpoint) for granular binning
stop     int     500     Ending (right endpoint) for granular binning
summaryCoverageThreshold     int[]     [15]     for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.

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.