Generate coverage summary information for reads data
Category Coverage Analysis
OverviewAssess 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.
- One or more bam files (with proper headers) to be analyzed for coverage statistics
- (Optional) A REFSEQ file to aggregate coverage to the gene level (for information about creating the REFSEQ file, please consult the online documentation)
Tables pertaining to different coverage summaries. Suffix on the table files declares the contents:
- no suffix: per locus coverage
- _summary: total, mean, median, quartiles, and threshold proportions, aggregated over all bases
- _statistics: coverage histograms (# locus with X coverage), aggregated over all bases
- _interval_summary: total, mean, median, quartiles, and threshold proportions, aggregated per interval
- _interval_statistics: 2x2 table of # of intervals covered to >= X depth in >=Y samples
- _gene_summary: total, mean, median, quartiles, and threshold proportions, aggregated per gene
- _gene_statistics: 2x2 table of # of genes covered to >= X depth in >= Y samples
- _cumulative_coverage_counts: coverage histograms (# locus with >= X coverage), aggregated over all bases
- _cumulative_coverage_proportions: proprotions of loci with >= X coverage, aggregated over all bases
- DepthOfCoverage currently only supports typical nucleotide (and N) bases, IUPAC ambiguity codes or other non-ATCGN bases will cause exceptions
- Read filters are applied to the reads before being counted in coverage information. By default Duplicate Marked and non-primary alignments are not counted. This can be disabled with --disable-tool-default-read-filters.
gatk \ DepthOfCoverage \ -R reference.fasta \ -O file_name_base \ -I input_bams.list [-geneList refSeq.sorted.refseq] \ [-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.
DepthOfCoverage specific arguments
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|
|BAM/SAM/CRAM file containing reads|
|One or more genomic intervals over which to operate|
|Base file location to which to write coverage summary information, must be a path to a file|
|Reference sequence file|
|Optional Tool Arguments|
||read one or more arguments files and add them to the command line|
|Calculate coverage statistics over this list of genes|
|-1||Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.|
|40||Size of the cloud-only prefetch buffer (in MB; 0 to disable).|
||COUNT_READS||How should overlapping reads from the same fragment be handled? NOTE: currently only COUNT_READS is supported|
|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.|
||false||If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!|
|20||If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection|
||Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.|
|false||display the help message|
|ALL||Interval merging rule for abutting intervals|
||127||Maximum quality of bases to count towards depth|
||0||Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.|
||0||Minimum quality of bases to count towards depth|
||false||Do not output depth of coverage at each base|
||false||Do not output gene summary if it was not completely covered by traversal intervals|
||false||Do not calculate per-interval statistics|
||false||Do not calculate per-sample per-depth counts of loci|
||false||Do not output the summary files per-sample|
||CSV||The format of the output file|
|[sample]||Partition type for depth of coverage|
||false||Add base counts to per-locus output|
||false||If true, don't emit genotype fields when writing vcf file output.|
||false||display the version number for this tool|
|Optional Common Arguments|
||true||If true, adds a PG tag to created SAM/BAM/CRAM files.|
||true||If true, adds a command line header line to created VCF files.|
|true||If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.|
|false||If true, create a MD5 digest for any BAM/SAM/CRAM file created|
|true||If true, create a VCF index when writing a coordinate-sorted VCF file.|
|false||If true, create a a MD5 digest any VCF file created.|
|Read filters to be disabled before analysis|
||false||Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)|
|One or more genomic intervals to exclude from processing|
||A configuration file to use with the GATK.|
|0||Amount of padding (in bp) to add to each interval you are excluding.|
|0||Amount of padding (in bp) to add to each interval you are including.|
|UNION||Set merging approach to use for combining interval inputs|
|false||Lenient processing of VCF files|
||false||Whether to suppress job-summary info on System.err.|
|Read filters to be applied before analysis|
||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.|
|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.|
||10.0||Output traversal statistics every time this many seconds elapse|
||Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.|
||Temp directory to use.|
|false||Whether to use the JdkDeflater (as opposed to IntelDeflater)|
|false||Whether to use the JdkInflater (as opposed to IntelInflater)|
||INFO||Control verbosity of logging.|
||false||Ignore sites consisting only of deletions|
||false||Include information on deletions alongside other bases in output table counts|
||false||Include sites where the reference is N|
||499||Number of bins to use for granular binning|
||false||display hidden arguments|
||1||Starting (left endpoint) for granular binning|
||500||Ending (right endpoint) for granular binning|
||||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.
--add-output-sam-program-record / -add-output-sam-program-record
If true, adds a PG tag to created SAM/BAM/CRAM files.
--add-output-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
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
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
--cloud-index-prefetch-buffer / -CIPB
int -1 [ [ -∞ ∞ ] ]
--cloud-prefetch-buffer / -CPB
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:
- Count all reads independently (even if from the same fragment).
- Count all fragments (even if the reads that compose the fragment are not consistent at that base).
- Count all fragments (but only if the reads that compose the fragment are consistent at that base).
--create-output-bam-index / -OBI
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
--create-output-bam-md5 / -OBM
If true, create a MD5 digest for any BAM/SAM/CRAM file created
If true, create a VCF index when writing a coordinate-sorted VCF file.
--create-output-variant-md5 / -OVM
If true, create a a MD5 digest any VCF file created.
--disable-bam-index-caching / -DBIC
--disable-read-filter / -DF
Read filters to be disabled before analysis
--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation
--disable-tool-default-read-filters / -disable-tool-default-read-filters
--exclude-intervals / -XL
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).
A configuration file to use with the GATK.
--gcs-max-retries / -gcs-retries
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.
--help / -h
display the help message
Ignore sites consisting only of deletions
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.
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.
--input / -I
BAM/SAM/CRAM file containing reads
R List[String] 
--interval-exclusion-padding / -ixp
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 / -imr
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:
--interval-padding / -ip
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 [ [ -∞ ∞ ] ]
--interval-set-rule / -isr
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:
- Take the union of all intervals
- Take the intersection of intervals (the subset that overlaps all intervals specified)
--intervals / -L
One or more genomic intervals over which to operate
R List[String] 
--lenient / -LE
Lenient processing of VCF files
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 ] ]
--max-depth-per-sample / -max-depth-per-sample
Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.
int 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.
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.
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
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.
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.
--output / -O
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:
--partition-type / -pt
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.
Add base counts to per-locus output
Instead of reporting depth, the program will report the base pileup at each locus
Whether to suppress job-summary info on System.err.
--read-filter / -RF
Read filters to be applied before analysis
--read-index / -read-index
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
--reference / -R
Reference sequence file
R GATKPathSpecifier null
--seconds-between-progress-updates / -seconds-between-progress-updates
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
--sequence-dictionary / -sequence-dictionary
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--showHidden / -showHidden
display hidden arguments
If true, don't emit genotype fields when writing vcf file output.
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.
Temp directory to use.
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
display the version number for this tool
GATK version 220.127.116.11-SNAPSHOT built at Fri, 24 Apr 2020 12:01:12 -0400.