Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T DiagnoseTargets -R reference.fasta -I sample1.bam -I sample2.bam -I sample3.bam -L intervals.interval_list -o output.vcf


Manual

Argument name(s)Default valueSummary
Optional Outputs
--missing_intervals
 -missing
NAProduces a file with the intervals that don't pass filters
--out
 -o
stdoutFile to which interval statistics should be written
Optional Parameters
--bad_mate_status_threshold
 -stBM
0.5The proportion of the loci needed for calling BAD_MATE
--coverage_status_threshold
 -stC
0.2The proportion of the loci needed for calling LOW_COVERAGE and COVERAGE_GAPS
--excessive_coverage_status_threshold
 -stXC
0.2The proportion of the loci needed for calling EXCESSIVE_COVERAGE
--maximum_coverage
 -max
1073741823The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE
--maximum_insert_size
 -ins
500The maximum allowed distance between a read and its mate
--minimum_base_quality
 -BQ
20The minimum Base Quality that is considered for calls
--minimum_coverage
 -min
5The minimum allowable coverage, used for calling LOW_COVERAGE
--minimum_mapping_quality
 -MQ
20The minimum read mapping quality considered for calls
--quality_status_threshold
 -stQ
0.5The proportion of the loci needed for calling POOR_QUALITY
--voting_status_threshold
 -stV
0.5The needed proportion of samples containing a call for the interval to adopt the call


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