Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, or library
This tool 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.
Tables pertaining to different coverage summaries. Suffix on the table files declares the contents:
java -jar GenomeAnalysisTK.jar \ -T DepthOfCoverage \ -R reference.fasta \ -o file_name_base \ -I input_bams.list [-geneList refSeq.sorted.txt] \ [-pt readgroup] \ [-ct 4 -ct 6 -ct 10] \ [-L my_capture_genes.interval_list]
These Read Filters are automatically applied to the data by the Engine before processing by DepthOfCoverage.
This tool can be run in multi-threaded mode using this option.
This tool does not apply any downsampling by default.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Outputs | |||
| --out -o |
None | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --calculateCoverageOverGenes -geneList |
NA | Calculate coverage statistics over this list of genes | |
| --countType |
COUNT_READS | How should overlapping reads from the same fragment be handled? | |
| --maxBaseQuality |
127 | Maximum quality of bases to count towards depth | |
| --maxMappingQuality |
2147483647 | Maximum mapping quality of reads to count towards depth | |
| --minBaseQuality -mbq |
-1 | Minimum quality of bases to count towards depth | |
| --minMappingQuality -mmq |
-1 | Minimum mapping quality of reads to count towards depth | |
| --outputFormat |
rtable | The format of the output file | |
| --partitionType -pt |
[sample] | Partition type for depth of coverage | |
| Optional Flags | |||
| --omitDepthOutputAtEachBase -omitBaseOutput |
false | Do not output depth of coverage at each base | |
| --omitIntervalStatistics -omitIntervals |
false | Do not calculate per-interval statistics | |
| --omitLocusTable |
false | Do not calculate per-sample per-depth counts of loci | |
| --omitPerSampleStats -omitSampleSummary |
false | Do not output the summary files per-sample | |
| --printBaseCounts -baseCounts |
false | Add base counts to per-locus output | |
| Advanced Parameters | |||
| --nBins |
499 | Number of bins to use for granular binning | |
| --start |
1 | Starting (left endpoint) for granular binning | |
| --stop |
500 | Ending (right endpoint) for granular binning | |
| --summaryCoverageThreshold -ct |
[15] | Coverage threshold (in percent) for summarizing statistics | |
| Advanced Flags | |||
| --ignoreDeletionSites |
false | Ignore sites consisting only of deletions | |
| --includeDeletions -dels |
false | Include information on deletions | |
| --includeRefNSites |
false | Include sites where the reference is N | |
| --printBinEndpointsAndExit |
false | Print the bin values and exit immediately | |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Calculate coverage statistics over this list of genes
Specify a RefSeq file for use in aggregating coverage statistics over genes.
This argument is incompatible with --calculateCoverageOverGenes and --omitIntervalStatistics. A warning will be logged and no output file will be produced for the gene list if these arguments are enabled together.
File NA
How should overlapping reads from the same fragment be handled?
The --countType argument is an enumerated type (CountPileupType), which can have one of the following values:
CountPileupType COUNT_READS
Ignore sites consisting only of deletions
boolean false
Include information on deletions
Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output.
boolean false
Include sites where the reference is N
Normally, sites where the reference is N (or another non-canonical base) are skipped. If this option is enabled, these sites will be included in DoC calculations if there is coverage from neighboring reads.
boolean false
Maximum quality of bases to count towards depth
Bases with quality scores higher than this threshold will be skipped. The default value is the largest number that can be represented as a byte.
byte 127 [ [ 0 127 ] ]
Maximum mapping quality of reads to count towards depth
Reads with mapping quality values higher than this threshold will be skipped. The default value is the largest number that can be represented as an integer by the program.
int 2147483647 [ [ 0 2,147,483,647 ] ]
Minimum quality of bases to count towards depth
Bases with quality scores lower than this threshold will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
byte -1 [ [ 0 127 ] ]
Minimum mapping quality of reads to count towards depth
Reads with mapping quality values lower than this threshold will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
int -1 [ [ 0 2,147,483,647 ] ]
Number of bins to use for granular binning
Sets the number of bins for granular binning
int 499 [ [ 0 [ 1 ∞ ] ]
Do not output depth of coverage at each base
Disabling the tabulation of total coverage at every base should speed up processing.
boolean false
Do not calculate per-interval statistics
Disabling the tabulation of interval statistics (mean, median, quartiles AND # intervals by sample by coverage) should speed up processing. This option is required in order to use -nt parallelism.
boolean false
Do not calculate per-sample per-depth counts of loci
Disabling the tabulation of locus statistics (# loci covered by sample by coverage) should speed up processing.
boolean false
Do not output the summary files per-sample
This option simply disables writing separate files for per-sample summary statistics (total, mean, median, quartile coverage per sample). These statistics are still calculated internally, so enabling this option will not improve runtime.
boolean false
An output file created by the walker. Will overwrite contents if file exists
Map[DoCOutputType,PrintStream] None
The format of the output file
Output file format (e.g. csv, table, rtable); defaults to r-readable table.
String rtable
Partition type for depth of coverage
By default, coverage is partitioning by sample, but it can be any combination of sample, readgroup and/or library.
Set[Partition] [sample]
Add base counts to per-locus output
Instead of reporting depth, the program will report the base pileup at each locus
boolean false
Print the bin values and exit immediately
Use this option to calibrate what bins you want before performing full calculations on your data.
boolean false
Starting (left endpoint) for granular binning
Sets the low-coverage cutoff for granular binning. All loci with depth < START are counted in the first bin.
int 1 [ [ 0 ∞ ] ]
Ending (right endpoint) for granular binning
Sets the high-coverage cutoff for granular binning. All loci with depth > STOP are counted in the last bin.
int 500 [ [ 1 ∞ ] ]
Coverage threshold (in percent) for summarizing statistics
For summary file outputs, report the percentage of bases covered to an amount equal to or greater than this number (e.g. % bases >= CT for each sample). Defaults to 15; can take multiple arguments.
int[] [15]