DiagnoseTargets

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

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy INTERVAL

Introduction

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

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

Additional Information

Read filters

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

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).

CommandLineGATK

DiagnoseTargets specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Required
--out	VariantContextWriter	stdout	File to which variants should be written
Optional
--bad_mate_status_threshold	double	0.5	The percentage of the loci needed for calling BAD_MATE
--coverage_status_threshold	double	0.2	The percentage of the loci needed for calling LOW_COVERAGE and COVERAGE_GAPS
--maximum_coverage	int	700	The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE
--maximum_insert_size	int	500	The maximum allowed distance between a read and its mate
--minimum_base_quality	int	20	The minimum Base Quality that is considered for calls
--minimum_coverage	int	5	The minimum allowable coverage, used for calling LOW_COVERAGE
--minimum_mapping_quality	int	20	The minimum read mapping quality considered for calls
--minimum_median_depth	int	10	The minimum allowable median coverage, used for calling LOW_MEDIAN_DEPTH
--print_debug_log	boolean	false	Used only for debugging the walker. Prints extra info to screen
--quality_status_threshold	double	0.5	The percentage of the loci needed for calling POOR_QUALITY
-stMED	double	0.2	The percentage of the loci needed for calling LOW_MEDIAN_DEPTH
-stXC	double	0.2	The percentage of the loci needed for calling EXCESSIVE_COVERAGE
--voting_status_threshold	double	0.5	The needed percentage 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.