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.
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.
|--variant||RodBinding[VariantContext]||NA||Input VCF file|
|--minCoverage||int||10||only samples that have coverage bigger than minCoverage will be counted|
|--OutputIntervals||PrintStream||stdout||Name of file for output intervals|
|--percentageOfSamples||double||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.
Name of file for output intervals.
only sites where at least percentageOfSamples of the samples have good coverage, will be emitted.
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). --variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.