Analyze coverage distribution and validate read mates per interval and per sample
This tool is useful for diagnosing regions with bad coverage, mapping, or read mate pairs. It analyzes each sample independently and aggregates results over intervals of interest. Low-coverage regions can be identified by using e.g. FindCoveredIntervals with the -uncovered argument.
A modified VCF detailing each interval by sample and information for each interval according to the thresholds used. Interval information includes GC Content, average interval depth, callable status among others. If you use the --missing option, you can get as a second output a intervals file with the loci that have missing data. This file can then be used as input to QualifyMissingIntervals for full qualification and interpretation of why the data is missing.
java -jar GenomeAnalysisTK.jar
-T DiagnoseTargets \
-R reference.fasta \
-I sample1.bam \
-I sample2.bam \
-I sample3.bam \
-L intervals.interval_list \
-o output.vcf
These Read Filters are automatically applied to the data by the Engine before processing by DiagnoseTargets.
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 | |||
| --missing_intervals -missing |
NA | Produces a file with the intervals that don't pass filters | |
| --out -o |
stdout | File to which interval statistics should be written | |
| Optional Parameters | |||
| --bad_mate_status_threshold -stBM |
0.5 | The proportion of the loci needed for calling BAD_MATE | |
| --coverage_status_threshold -stC |
0.2 | The proportion of the loci needed for calling LOW_COVERAGE and COVERAGE_GAPS | |
| --excessive_coverage_status_threshold -stXC |
0.2 | The proportion of the loci needed for calling EXCESSIVE_COVERAGE | |
| --maximum_coverage -max |
1073741823 | The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE | |
| --maximum_insert_size -ins |
500 | The maximum allowed distance between a read and its mate | |
| --minimum_base_quality -BQ |
20 | The minimum Base Quality that is considered for calls | |
| --minimum_coverage -min |
5 | The minimum allowable coverage, used for calling LOW_COVERAGE | |
| --minimum_mapping_quality -MQ |
20 | The minimum read mapping quality considered for calls | |
| --quality_status_threshold -stQ |
0.5 | The proportion of the loci needed for calling POOR_QUALITY | |
| --voting_status_threshold -stV |
0.5 | The needed proportion of samples containing a call for the interval to adopt the call | |
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.
The proportion of the loci needed for calling BAD_MATE
The proportion of reads in the loci that must have bad mates for the sample to be reported as BAD_MATE
double 0.5 [ [ -∞ ∞ ] ]
The proportion of the loci needed for calling LOW_COVERAGE and COVERAGE_GAPS
The proportion of loci in a sample that must fall under the LOW_COVERAGE or COVERAGE_GAPS category for the sample to be reported as either (or both)
double 0.2 [ [ -∞ ∞ ] ]
The proportion of the loci needed for calling EXCESSIVE_COVERAGE
The proportion of loci in a sample that must fall under the EXCESSIVE_COVERAGE category for the sample to be reported as EXCESSIVE_COVERAGE
double 0.2 [ [ -∞ ∞ ] ]
The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE
If at any locus, a sample has more coverage than this, it will be reported as EXCESSIVE_COVERAGE
int 1073741823 [ [ -∞ ∞ ] ]
The maximum allowed distance between a read and its mate
If any sample has a paired read whose distance between alignment starts (between the pairs) is greater than this, it will be reported as BAD_MATE
int 500 [ [ -∞ ∞ ] ]
The minimum Base Quality that is considered for calls
Only bases with quality greater than this will be considered in the coverage metrics.
int 20 [ [ -∞ ∞ ] ]
The minimum allowable coverage, used for calling LOW_COVERAGE
If at any locus, a sample has less coverage than this, it will be reported as LOW_COVERAGE
int 5 [ [ -∞ ∞ ] ]
The minimum read mapping quality considered for calls
Only reads with mapping quality greater than this will be considered in the coverage metrics.
int 20 [ [ -∞ ∞ ] ]
Produces a file with the intervals that don't pass filters
PrintStream NA
File to which interval statistics should be written
VariantContextWriter stdout
The proportion of the loci needed for calling POOR_QUALITY
The proportion of loci in a sample that must fall under the LOW_QUALITY category for the sample to be reported as LOW_QUALITY
double 0.5 [ [ -∞ ∞ ] ]
The needed proportion of samples containing a call for the interval to adopt the call
The proportion of samples that must have a status for it to filter the entire interval. Example: 8 out of 10 samples have low coverage status on the interval,
with a threshold higher than 0.2, this interval will be filtered as LOW_COVERAGE.
double 0.5 [ [ -∞ ∞ ] ]