Generate coverage summary information for reads data
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:
gatk \ DepthOfCoverage \ -R reference.fasta \ -O file_name_base \ -I input_bams.list [-gene-list refSeq.sorted.refseq] \ [-partition-type readgroup] \ [--summary-coverage-threshold 4 --summary-coverage-threshold 6 --summary-coverage-threshold 10] \ [-L my_capture_genes.interval_list]
These Read Filters are automatically applied to the data by the Engine before processing by DepthOfCoverage.
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 | |
|---|---|---|---|
| Required Arguments | |||
| --input -I |
BAM/SAM/CRAM file containing reads | ||
| --intervals -L |
One or more genomic intervals over which to operate | ||
| --output -O |
Base file location to which to write coverage summary information, must be a path to a file | ||
| --reference -R |
Reference sequence file | ||
| Optional Tool Arguments | |||
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --calculate-coverage-over-genes -gene-list |
Calculate coverage statistics over this list of genes | ||
| --cloud-index-prefetch-buffer -CIPB |
-1 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. | |
| --cloud-prefetch-buffer -CPB |
40 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). | |
| --count-type |
COUNT_READS | How should overlapping reads from the same fragment be handled? NOTE: currently only COUNT_READS is supported | |
| --disable-bam-index-caching -DBIC |
false | If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. | |
| --disable-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
| --gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
| --gcs-project-for-requester-pays |
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed. | ||
| --help -h |
false | display the help message | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --max-base-quality |
127 | Maximum quality of bases to count towards depth | |
| --max-depth-per-sample |
0 | Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable. | |
| --min-base-quality |
0 | Minimum quality of bases to count towards depth | |
| --omit-depth-output-at-each-base |
false | Do not output depth of coverage at each base | |
| --omit-genes-not-entirely-covered-by-traversal |
false | Do not output gene summary if it was not completely covered by traversal intervals | |
| --omit-interval-statistics |
false | Do not calculate per-interval statistics | |
| --omit-locus-table |
false | Do not calculate per-sample per-depth counts of loci | |
| --omit-per-sample-statistics |
false | Do not output the summary files per-sample | |
| --output-format |
CSV | The format of the output file | |
| --partition-type -pt |
[sample] | Partition type for depth of coverage | |
| --print-base-counts |
false | Add base counts to per-locus output | |
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --add-output-sam-program-record |
true | If true, adds a PG tag to created SAM/BAM/CRAM files. | |
| --add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
| --create-output-bam-index -OBI |
true | If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. | |
| --create-output-bam-md5 -OBM |
false | If true, create a MD5 digest for any BAM/SAM/CRAM file created | |
| --create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
| --create-output-variant-md5 -OVM |
false | If true, create a a MD5 digest any VCF file created. | |
| --disable-read-filter -DF |
Read filters to be disabled before analysis | ||
| --disable-tool-default-read-filters |
false | Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) | |
| --exclude-intervals -XL |
One or more genomic intervals to exclude from processing | ||
| --gatk-config-file |
A configuration file to use with the GATK. | ||
| --interval-exclusion-padding -ixp |
0 | Amount of padding (in bp) to add to each interval you are excluding. | |
| --interval-padding -ip |
0 | Amount of padding (in bp) to add to each interval you are including. | |
| --interval-set-rule -isr |
UNION | Set merging approach to use for combining interval inputs | |
| --inverted-read-filter -XRF |
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters). | ||
| --lenient -LE |
false | Lenient processing of VCF files | |
| --max-variants-per-shard |
0 | If non-zero, partitions VCF output into shards, each containing up to the given number of records. | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --read-filter -RF |
Read filters to be applied before analysis | ||
| --read-index |
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. | ||
| --read-validation-stringency -VS |
SILENT | Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --seconds-between-progress-updates |
10.0 | Output traversal statistics every time this many seconds elapse | |
| --sequence-dictionary |
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. | ||
| --tmp-dir |
Temp directory to use. | ||
| --use-jdk-deflater -jdk-deflater |
false | Whether to use the JdkDeflater (as opposed to IntelDeflater) | |
| --use-jdk-inflater -jdk-inflater |
false | Whether to use the JdkInflater (as opposed to IntelInflater) | |
| --verbosity |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --ignore-deletion-sites |
false | Ignore sites consisting only of deletions | |
| --include-deletions |
false | Include information on deletions alongside other bases in output table counts | |
| --include-ref-n-sites |
false | Include sites where the reference is N | |
| --nBins |
499 | Number of bins to use for granular binning | |
| --showHidden |
false | display hidden arguments | |
| --start |
1 | Starting (left endpoint) for granular binning | |
| --stop |
500 | Ending (right endpoint) for granular binning | |
| --summary-coverage-threshold |
[15] | Coverage threshold (in percent) for summarizing statistics | |
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.
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
If true, adds a command line header line to created VCF files.
boolean true
read one or more arguments files and add them to the command line
List[File] []
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 --omit-interval-statistics. A warning will be logged and no output file will be produced for the gene list if these arguments are enabled together.
Exclusion: This argument cannot be used at the same time as omit-interval-statistics.
List[String] []
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
How should overlapping reads from the same fragment be handled? NOTE: currently only COUNT_READS is supported
The --count-type argument is an enumerated type (CountPileupType), which can have one of the following values:
CountPileupType COUNT_READS
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
If true, create a a MD5 digest any VCF file created.
boolean false
If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
boolean false
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the
command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals
(e.g. -XL myFile.intervals). strings gathered from the command line -XL argument to be parsed into intervals to exclude
List[String] []
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.
String ""
display the help message
boolean false
Ignore sites consisting only of deletions
boolean false
Include information on deletions alongside other bases in output table counts
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
BAM/SAM/CRAM file containing reads
R List[GATKPath] []
Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a
padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not
actually overlap) into a single continuous interval. However you can change this behavior if you want them to be
treated as separate intervals instead.
The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:
IntervalMergingRule ALL
Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a
padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can
change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to
perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule
INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will
always be merged using UNION).
Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.
The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:
IntervalSetRule UNION
One or more genomic intervals over which to operate
R List[String] []
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
List[String] []
Lenient processing of VCF files
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 number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.
int 0 [ [ -∞ ∞ ] ]
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
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 0 [ [ 0 127 ] ]
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 output gene summary if it was not completely covered by traversal intervals
Remove genes from the gene summary output file if all of its exon bases were not completely covered by traversal.
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.
Exclusion: This argument cannot be used at the same time as calculate-coverage-over-genes.
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
Base file location to which to write coverage summary information, must be a path to a file
Base file name about which to create the coverage information
R String null
The format of the output file
Output file format (e.g. csv, table, rtable); defaults to r-readable table.
The --output-format argument is an enumerated type (DEPTH_OF_COVERAGE_OUTPUT_FORMAT), which can have one of the following values:
DEPTH_OF_COVERAGE_OUTPUT_FORMAT CSV
Partition type for depth of coverage
By default, coverage is partitioned by sample, but it can be any combination of sample, readgroup and/or library.
The --partition-type argument is an enumerated type (EnumSet[Partition]), which can have one of the following values:
EnumSet[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
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
List[GATKPath] []
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
ValidationStringency SILENT
Reference sequence file
R GATKPath null
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
GATKPath null
display hidden arguments
boolean false
If true, don't emit genotype fields when writing vcf file output.
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.
List[Integer] [15]
Temp directory to use.
GATKPath null
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.