java -jar GenomeAnalysisTK.jar

Category

Genome Variant Analysis

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Usage

java -jar GenomeAnalysisTK.jar -T FindCoveredIntervals -R reference.fasta -I my_file.bam [-cov 10 \] [-uncovered \] -o output.list

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Manual

Argument name(s)	Default value	Summary
Optional Outputs
--activeRegionOut  -ARO	NA	Output the active region to this IGV formatted file
--activityProfileOut  -APO	NA	Output the raw activity profile results in IGV format
--out  -o	stdout	An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--coverage_threshold  -cov	20	The minimum allowable coverage to be considered covered
--minBaseQuality  -minBQ	0	The minimum allowable base quality score to be counted for coverage
--minMappingQuality  -minMQ	0	The minimum allowable mapping quality score to be counted for coverage
Optional Flags
--uncovered  -u	false	output intervals that fail the coverage threshold instead
Advanced Inputs
--activeRegionIn  -AR	NA	Use this interval list file as the active regions to process
Advanced Parameters
--activeProbabilityThreshold  -ActProbThresh	0.002	Threshold for the probability of a profile state being active.
--activeRegionExtension	NA	The active region extension; if not provided defaults to Walker annotated default
--activeRegionMaxSize	NA	The active region maximum size; if not provided defaults to Walker annotated default
--bandPassSigma	NA	The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default
--maxReadsInMemoryPerSample	30000	Maximum reads per sample given to traversal map() function
--maxTotalReadsInMemory	10000000	Maximum total reads given to traversal map() function
Advanced Flags
--forceActive	false	If provided, all bases will be tagged as active

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