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. |
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration
Repository package_gatk_1_4 revision ec95ec570854 owned by devteam |
Repository package_samtools_0_1_18 revision 171cd8bc208d owned by devteam |
Name | Version | Type | |
---|---|---|---|
gatk | 1.4 | package | |
samtools | 0.1.18 | package |
Name | Description | Version | Minimum Galaxy Version |
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on BAM files | 0.0.5 | any |