Repository table_recalibration
Owner: devteam
Synopsis: Table Recalibration on BAM files
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.
Type: unrestricted
Revision: 1:30e1dd77e99c
This revision can be installed: True
Times cloned / installed: 2806
Dependencies of this repository

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

Contents of this repository

Name Description Version Minimum Galaxy Version
on BAM files 0.0.5 any

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis