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Revision as of 16:50, 22 October 2014
, 16:50, 22 October 2014→Alignment Pipeline Output
=== Alignment Pipeline Output ===
=== Alignment Pipeline Output ===
Upon successful completion of the alignment pipeline, you should see the following files/ subdirectories under the user specified output directory:
Upon successful completion of the alignment pipeline, you should see the following files/ subdirectories under the user specified output directory:
* '''bam.list''' - file containing sample -> BAM mapping that can be used in other GotCloud pipelines
* '''bam.list''' - file containing sample->BAM mapping that can be used in other GotCloud pipelines
* '''bams/''' - contains the final BAM and bai (BAM index) files
* '''bams/''' - contains the final BAM and bai (BAM index) files
** '''*.recal.bam'''
** '''*.recal.bam'''
* Makefiles/ - contains the Makefiles and logs used by GotCloud to run the alignment pipeline
* Makefiles/ - contains the Makefiles and logs used by GotCloud to run the alignment pipeline
* '''QCFiles/''' - contains quality control results if quality control is not disabled
* '''QCFiles/''' - contains quality control results if quality control is not disabled
**
** 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
* tmp/ - contains intermediate files (most are deleted unless --keepTmp is specified)
* tmp/ - contains intermediate files (most are deleted unless --keepTmp is specified)
* *.OK - one OK file per sample; indicates the Sample successfully completed alignment
* *.OK - one OK file per sample; indicates the Sample successfully completed alignment
