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Revision as of 21:14, 18 March 2015
, 21:14, 18 March 2015→Outputs
====Outputs====
====Outputs====
Upon successful completion of the *recab* sub-pipeline, you should see the following files/subdirectories under the user specified output directory:
Upon successful completion of the *recabQC* sub-pipeline, you should see the following files/subdirectories under the user specified output directory:
*'''recab/mergedBams/''' - contains merge results
*'''recab/mergedBams/''' - contains merge results
** '''''*/SAMPLE.merged.bam'' - a merged BAM file'''
** '''''*/SAMPLE.merged.bam'' - a merged BAM file'''
*** '''''*/SAMPLE.qplot.stats'' - sample statistics'''
*** '''''*/SAMPLE.qplot.stats'' - sample statistics'''
You should see .done and .OK files for each SAMPLE in the index file. If you do not see the .done and .OK files, then your *recab* sub-pipeline failed.
You should see .done and .OK files for each SAMPLE in the index file. If you do not see the .done and .OK files, then your *recabQC* sub-pipeline failed.
'''On success, the recab/ folder contains the final BAMs and bais.'''
'''On success, the recab/ folder contains the final BAMs and bais, while the QCFiles/ folder contains the quality control output'''
===Command-Line and Configuration Options===
===Command-Line and Configuration Options===
