Walks along reference and calculates a few metrics for each interval.
A reference file (for GC content), the input bam file (for base and mapping quality calculation), the missing intervals (in the -L), the baits/targets used to sequence (in the -targets) and a bed file with the coding sequence intervals of the genome (in the -cds)
GC content, distance from the end of the target, coding sequence intersection, mapping and base quality averages and average depth per "missing" interval.
java -Xmx2g -jar GenomeAnalysisTK.jar \ -T QualifyMissingIntervals \ -R ref.fasta \ -I input.bam \ -o output.grp \ -L input.intervals \ -cds cds.intervals \ -targets targets.intervals
These Read Filters are automatically applied to the data by the Engine before processing by QualifyMissingIntervals.
This tool can be run in multi-threaded mode using this option.
This tool applies the following downsampling settings by default.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--out||PrintStream||stdout||An output file created by the walker. Will overwrite contents if file exists|
|--coveragethreshold||int||20||minimum coverage to be considered sequenceable|
|--gcthreshold||double||0.3||upper and lower bound for an interval to be considered high/low GC content|
|--intervalsizethreshold||byte||10||minimum interval length to be considered|
|--mappingthreshold||byte||20||minimum mapping quality for it to be considered usable|
|--qualthreshold||byte||20||minimum base quality for it to be considered usable|
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.
Undocumented option. List of baits to distinguish untargeted intervals from those that are targeted but not covered
minimum coverage to be considered sequenceable. The coverage of a missing interval may determine whether or not an interval is sequenceable. A low coverage will trigger gc content, mapping, base qualities and other checks to figure out why this interval was deemed unsequenceable.
upper and lower bound for an interval to be considered high/low GC content. This value will be used to determine whether or not an interval had too high or too low GC content to be sequenced. This is only applied if there was not enough data in the interval.
minimum interval length to be considered. Intervals that are too small generate biased analysis. For example an interval of size 1 will have GC content 1 or 0. To avoid misinterpreting small intervals, all intervals below this threshold will be ignored in the interpretation.
minimum mapping quality for it to be considered usable. An average mapping quality above this value will determine the interval to be mappable.
An output file created by the walker. Will overwrite contents if file exists. A single GATKReport table with the qualifications on why the intervals passed by the -L argument were missing.
minimum base quality for it to be considered usable. An average base quality above this value will rule out the possibility of context specific problems with the sequencer.
Undocumented option. List of targets used in the experiment. This file will be used to calculate the distance your missing intervals are to the targets (usually exons). Typically this is your hybrid selection targets file (e.g. Agilent exome target list)
GATK version 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.