What it does
This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker.
For more information on base quality score recalibration using the GATK, see this tool specific page.
To learn about best practices for variant detection using GATK, see this overview.
If you encounter errors, please view the GATK FAQ.
Inputs
GenomeAnalysisTK: TableRecalibration accepts an aligned BAM and a recalibration CSV input files.
Outputs
The output is in BAM format.
Go here for details on GATK file formats.
Settings:
default_read_group If a read has no read group then default to the provided String. default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid. force_read_group If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group. force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid. window_size_nqs The window size used by MinimumNQSCovariate for its calculation homopolymer_nback The number of previous bases to look at in HomopolymerCovariate exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1 solid_recal_mode How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS) solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ) recal_file Filename for the input covariates table recalibration .csv file out The output BAM file bam_compression Compression level to use for writing BAM files disable_bam_indexing Turn off on-the-fly creation of indices for output BAM files. simplifyBAM If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier preserve_qscores_less_than Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases smoothing Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1 max_quality_score The integer value at which to cap the quality scores, default=50 doNotWriteOriginalQuals If true, we will not write the original quality (OQ) tag for each read
Citation
If you use this tool in Galaxy, please cite Blankenberg D, et al. In preparation.