For a complete, detailed argument reference, refer to the GATK document page here.
DepthOfCoverage is a coverage profiler for a (possibly multi-sample) bam file. It uses a granular histogram that can be user-specified to present useful aggregate coverage data. It reports the following metrics over the entire .bam file:
Because the common question "What proportion of my targeted bases are well-powered to discover SNPs?" is answered by the last matrix on the above list, it is strongly recommended that this walker be run on all samples simultaneously.
For humans, DepthOfCoverage can also be configured to output these statistics aggregated over genes, by providing it with a RefSeq ROD.
DepthOfCoverage also outputs, by default, the total coverage at every locus, and the coverage per sample and/or read group. This behavior can optionally be turned off, or switched to base count mode, where base counts will be output at each locus, rather than total depth.
To get a summary of coverage by each gene, you may supply a refseq (or alternative) gene list via the argument
The provided gene list must be of the following format:
585 NM_001005484 chr1 + 58953 59871 58953 59871 1 58953, 59871, 0 OR4F5 cmpl cmpl 0, 587 NM_001005224 chr1 + 357521 358460 357521 358460 1 357521, 358460, 0 OR4F3 cmpl cmpl 0, 587 NM_001005277 chr1 + 357521 358460 357521 358460 1 357521, 358460, 0 OR4F16 cmpl cmpl 0, 587 NM_001005221 chr1 + 357521 358460 357521 358460 1 357521, 358460, 0 OR4F29 cmpl cmpl 0, 589 NM_001005224 chr1 - 610958 611897 610958 611897 1 610958, 611897, 0 OR4F3 cmpl cmpl 0, 589 NM_001005277 chr1 - 610958 611897 610958 611897 1 610958, 611897, 0 OR4F16 cmpl cmpl 0, 589 NM_001005221 chr1 - 610958 611897 610958 611897 1 610958, 611897, 0 OR4F29 cmpl cmpl 0,
If you are on the broad network, the properly-formatted file containing refseq genes and transcripts is located at
If you supply the -geneList argument, DepthOfCoverage will output an additional summary file that looks as follows:
Gene_Name Total_Cvg Avg_Cvg Sample_1_Total_Cvg Sample_1_Avg_Cvg Sample_1_Cvg_Q3 Sample_1_Cvg_Median Sample_1_Cvg_Q1 SORT1 594710 238.27 594710 238.27 165 245 330 NOTCH2 3011542 357.84 3011542 357.84 222 399 >500 LMNA 563183 186.73 563183 186.73 116 187 262 NOS1AP 513031 203.50 513031 203.50 91 191 290
Note that the gene coverage will be aggregated only over samples (not read groups, libraries, or other types). The
-geneList argument also requires specific intervals within genes to be given (say, the particular exons you are interested in, or the entire gene), and it functions by aggregating coverage from the interval level to the gene level, by referencing each interval to the gene in which it falls. Because by-gene aggregation looks for intervals that overlap genes,
-geneList is ignored if
-omitIntervals is thrown.
We have decided to continue providing and supporting DepthOfCoverage and DiagnoseTargets for the foreseeable future. Going forward, we'll try to integrate them and develop their features to address the main needs of the community. To this end we welcome your continuing feedback, so please feel free to contribute comments and ideas in this thread.
To all who took the time to tell us what you find useful about DoC and DT (and what you wish it could do), a big thank you! This is always very useful to us because it helps us identify which features are most valuable to our users.