# DiagnoseTargets

Analyzes coverage distribution and validates read mates for a given interval and sample.

## Overview

Used to diagnose regions with bad coverage, mapping, or read mating. Analyzes each sample independently in addition to interval wide analysis.

### Input

• A reference file
• one or more input BAMs
• One or more intervals

### Output

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.

### Examples

    java
-jar GenomeAnalysisTK.jar
-T DiagnoseTargets \
-R reference.fasta \
-o output.vcf \
-I sample1.bam \
-I sample2.bam \
-I sample3.bam \
-L intervals.interval_list


These Read Filters are automatically applied to the data by the Engine before processing by DiagnoseTargets.

### Downsampling settings

This tool does not apply any downsampling by default.

## Command-line Arguments

### Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

### DiagnoseTargets 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
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
-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

### Argument details

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  [ [ -∞  ∞ ] ]

### --coverage_status_threshold / -stC

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  [ [ -∞  ∞ ] ]

### --excessive_coverage_status_threshold / -stXC

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  [ [ -∞  ∞ ] ]

### --maximum_coverage / -max

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  [ [ -∞  ∞ ] ]

### --maximum_insert_size / -ins

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  [ [ -∞  ∞ ] ]

### --minimum_base_quality / -BQ

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  [ [ -∞  ∞ ] ]

### --minimum_coverage / -min

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  [ [ -∞  ∞ ] ]

### --minimum_mapping_quality / -MQ

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  [ [ -∞  ∞ ] ]

### --missing_intervals / -missing

Produces a file with the intervals that don't pass filters

PrintStream

### --out / -o

File to which interval statistics should be written

VariantContextWriter  stdout

### --quality_status_threshold / -stQ

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  [ [ -∞  ∞ ] ]

### --voting_status_threshold / -stV

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  [ [ -∞  ∞ ] ]

GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA