AssessReducedQuals

Emits intervals in which the differences between the original and reduced bam quals are bigger epsilon (unless the quals of the reduced bam are above sufficient threshold)

Category Uncategorized

Traversal LocusWalker

PartitionBy LOCUS

Overview

Input

The original and reduced BAM files.

Output

A list of intervals in which the differences between the original and reduced bam quals are bigger epsilon.

Examples

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -I:original original.bam \
   -I:reduced reduced.bam \
   -R ref.fasta \
   -T AssessReducedQuals \
   -o output.intervals

Additional Information

Read filters

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

Parallelism options

This tool can be run in multi-threaded mode using this option.

TreeReducible (-nt)

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

AssessReducedQuals 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
Optional
--exclude_low_mq	int	0	ignore reads with mapping quality below this number
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists
--qual_epsilon	double	0.1	when \|Quals_reduced_bam - Quals_original_bam\| > (epsilon * Quals_original_bam) we output this interval
--sufficientQualSum	int	600	When a reduced bam qual sum is above this threshold, it passes even without comparing to the non-reduced bam

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.

--exclude_low_mq / -excludeMQ ( int with default value 0 )

ignore reads with mapping quality below this number.

--out / -o ( PrintStream with default value stdout )

An output file created by the walker. Will overwrite contents if file exists.

--qual_epsilon / -epsilon ( double with default value 0.1 )

when |Quals_reduced_bam - Quals_original_bam| > (epsilon * Quals_original_bam) we output this interval.

--sufficientQualSum / -sufficientQualSum ( int with default value 600 )

When a reduced bam qual sum is above this threshold, it passes even without comparing to the non-reduced bam .

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.