java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I my_reads.bam -knownSites latest_dbsnp.vcf -o recal_data.table
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Outputs | |||
| --out  -o | NA | The output recalibration table file to create | |
| Optional Inputs | |||
| --knownSites | [] | A database of known polymorphic sites | |
| Optional Parameters | |||
| --covariate  -cov | NA | One or more covariates to be used in the recalibration. Can be specified multiple times | |
| --indels_context_size  -ics | 3 | Size of the k-mer context to be used for base insertions and deletions | |
| --maximum_cycle_value  -maxCycle | 500 | The maximum cycle value permitted for the Cycle covariate | |
| --mismatches_context_size  -mcs | 2 | Size of the k-mer context to be used for base mismatches | |
| --solid_nocall_strategy | THROW_EXCEPTION | Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ | |
| --solid_recal_mode  -sMode | SET_Q_ZERO | How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS | |
| Optional Flags | |||
| --list  -ls | false | List the available covariates and exit | |
| --lowMemoryMode | false | Reduce memory usage in multi-threaded code at the expense of threading efficiency | |
| --no_standard_covs  -noStandard | false | Do not use the standard set of covariates, but rather just the ones listed using the -cov argument | |
| --sort_by_all_columns  -sortAllCols | false | Sort the rows in the tables of reports | |
| Advanced Parameters | |||
| --binary_tag_name  -bintag | NA | the binary tag covariate name if using it | |
| --bqsrBAQGapOpenPenalty  -bqsrBAQGOP | 40.0 | BQSR BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets | |
| --deletions_default_quality  -ddq | 45 | default quality for the base deletions covariate | |
| --insertions_default_quality  -idq | 45 | default quality for the base insertions covariate | |
| --low_quality_tail  -lqt | 2 | minimum quality for the bases in the tail of the reads to be considered | |
| --mismatches_default_quality  -mdq | -1 | default quality for the base mismatches covariate | |
| --quantizing_levels  -ql | 16 | number of distinct quality scores in the quantized output | |
| Advanced Flags | |||
| --run_without_dbsnp_potentially_ruining_quality | false | If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only. | |