Print intervals file with all the variant sites for which most of the samples have good coverage
CoveredByNSamplesSites is a GATK tool for filtering out sites based on their coverage. The sites that pass the filter are printed out to an intervals file. See argument defaults for what constitutes "most" samples and "good" coverage. These parameters can be modified from the command line.
A variant file and optionally min coverage and sample percentage values.
An intervals file.
java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T CoveredByNSamplesSites \ -V input.vcf \ -out output.intervals \ -minCov 15
These Read Filters are automatically applied to the data by the Engine before processing by CoveredByNSamplesSites.
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 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|
|NA||Input VCF file|
|stdout||Name of file for output intervals|
|10||only samples that have coverage bigger than minCoverage will be counted|
|0.9||only sites where at least percentageOfSamples of the samples have good coverage, will be emitted|
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.
only samples that have coverage bigger than minCoverage will be counted
int 10 [ [ -? ? ] ]
Name of file for output intervals
only sites where at least percentageOfSamples of the samples have good coverage, will be emitted
double 0.9 [ [ -? ? ] ]
Input VCF file
Variants from this VCF file are used by this tool as input. The file must at least contain the standard VCF header lines, but can be empty (i.e., no variants are contained in the file).
GATK version 3.0-0-g6bad1c6 built at 2014/03/06 06:38:04. GTD: NA