java -jar GenomeAnalysisTK.jar

Category

Genome Variant Analysis

---

Usage

java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R reference.fasta -o file_name_base -I input_bams.list [-geneList refSeq.sorted.txt] [-pt readgroup] [-ct 4 -ct 6 -ct 10] [-L my_capture_genes.interval_list]

---

Manual

Argument name(s)	Default value	Summary
Optional Outputs
--out  -o	None	An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--calculateCoverageOverGenes  -geneList	NA	Calculate coverage statistics over this list of genes
--countType	COUNT_READS	How should overlapping reads from the same fragment be handled?
--maxBaseQuality	127	Maximum quality of bases to count towards depth
--maxMappingQuality	2147483647	Maximum mapping quality of reads to count towards depth
--minBaseQuality  -mbq	-1	Minimum quality of bases to count towards depth
--minMappingQuality  -mmq	-1	Minimum mapping quality of reads to count towards depth
--outputFormat	rtable	The format of the output file
--partitionType  -pt	[sample]	Partition type for depth of coverage
Optional Flags
--omitDepthOutputAtEachBase  -omitBaseOutput	false	Do not output depth of coverage at each base
--omitIntervalStatistics  -omitIntervals	false	Do not calculate per-interval statistics
--omitLocusTable	false	Do not calculate per-sample per-depth counts of loci
--omitPerSampleStats  -omitSampleSummary	false	Do not output the summary files per-sample
--printBaseCounts  -baseCounts	false	Add base counts to per-locus output
Advanced Parameters
--nBins	499	Number of bins to use for granular binning
--start	1	Starting (left endpoint) for granular binning
--stop	500	Ending (right endpoint) for granular binning
--summaryCoverageThreshold  -ct	[15]	Coverage threshold (in percent) for summarizing statistics
Advanced Flags
--ignoreDeletionSites	false	Ignore sites consisting only of deletions
--includeDeletions  -dels	false	Include information on deletions
--includeRefNSites	false	Include sites where the reference is N
--printBinEndpointsAndExit	false	Print the bin values and exit immediately

---

Share your experience or ask a question