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