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Revision as of 21:26, 17 March 2015
, 21:26, 17 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 *recab* sub-pipeline, you should see the following files/subdirectories under the user specified output directory:
*'''recab/mergedBams/'''
*'''recab/mergedBams/''' - contains merge results
** '''''*/SAMPLE.merged.bam'' - a merged BAM file'''
** '''''*/SAMPLE.merged.bam'' - a merged BAM file'''
** ''*/SAMPLE.merged.bam.log'' - merge log
** ''*/SAMPLE.merged.bam.log'' - merge log
** ''*/SAMPLE.merged.bam.OK'' - temp file indicating the merge step completed successfully
** ''*/SAMPLE.merged.bam.OK'' - temp file indicating the merge step completed successfully
* '''recab/'''
* '''recab/''' - contains recalibration results
** '''''*/SAMPLE.recal.bam'' - a merged, recalibrated, and deduped BAM file'''
** '''''*/SAMPLE.recal.bam'' - a merged, recalibrated, and deduped BAM file'''
** '''''*/SAMPLE.recal.bam.bai'' - an indexed version of the merged, recalibrated, and deduped BAM file'''
** '''''*/SAMPLE.recal.bam.bai'' - an indexed version of the merged, recalibrated, and deduped BAM file'''
** ''*/SAMPLE.recal.bam.done'' - temp file indicating the recalibration step completed successfully
** ''*/SAMPLE.recal.bam.done'' - temp file indicating the recalibration step completed successfully
** ''*/SAMPLE.recal.bam.bai.done'' - temp file indicating the indexing step completed successfully
** ''*/SAMPLE.recal.bam.bai.done'' - temp file indicating the indexing step completed successfully
* '''QCFiles/''' - contains quality control results
** VerifyBamID Output - see [[VerifyBamID#A_guideline_to_interpret_output_files|VerifyBamID: A guideline to interpret output files]] for more information
*** *.genoCheck.depthRG - depth distribution of the sequence reads per read group
*** *.genoCheck.depthSM - depth distribution of the sequence reads per sample
*** ''*.genoCheck.done'' - temp file indicating this step completed successfully
*** *.genoCheck.selfRG - per-readGroup statistics describing how well each lane matches to the annotated sample
*** '''*.genoCheck.selfSM''' - main output file containing the contamination estimate; per-sample statistics describing how well the sample matches to the annotated sample
**** Check the 'FREEMIX' column for genotype-free estimate of contamination 0-1 scale, the lower, the better
**** If [FREEMIX] >= 0.03 and [FREELK1]-[FREELK0] is large, possible contamination
** Qplot Output - see: [[QPLOT#Diagnose_sequencing_quality|QPLOT: Diagnose sequencing quality]] for more info on how to use QPLOT results
*** ''*.qplot.done'' - temp file indicating this step completed successfully
*** '''*.qplot.R''' - Rscript that can be used to generate the pdf graphs
*** '''*.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 *recab* sub-pipeline failed.
