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Revision as of 21:31, 17 March 2015
, 21:31, 17 March 2015→Outputs
* '''QCFiles/''' - contains quality control results
* '''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
** VerifyBamID Output - see [[VerifyBamID#A_guideline_to_interpret_output_files|VerifyBamID: A guideline to interpret output files]] for more information
*** */SAMPLE.genoCheck.depthRG - depth distribution of the sequence reads per read group
*** ''*/SAMPLE.genoCheck.depthRG'' - depth distribution of the sequence reads per read group
*** */SAMPLE.genoCheck.depthSM - depth distribution of the sequence reads per sample
*** ''*/SAMPLE.genoCheck.depthSM'' - depth distribution of the sequence reads per sample
*** ''*/SAMPLE.genoCheck.err'' - ?
*** ''*/SAMPLE.genoCheck.log'' - ?
*** ''*/SAMPLE.genoCheck.OK'' - temp file indicating the VerifyBAMID step completed successfully
*** ''*/SAMPLE.genoCheck.OK'' - temp file indicating the VerifyBAMID step completed successfully
*** */SAMPLE.genoCheck.selfRG - per-readGroup statistics describing how well each lane matches to the annotated sample
*** ''*/SAMPLE.genoCheck.selfRG'' - per-readGroup statistics describing how well each lane matches to the annotated sample
*** '''*/SAMPLE.genoCheck.selfSM''' - main output file containing the contamination estimate; per-sample statistics describing how well the sample matches to the annotated sample
*** '''''*/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
**** 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
**** 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 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
*** ''*/SAMPLE.qplot.OK'' - temp file indicating the qplot step completed successfully
*** '''*.qplot.R''' - Rscript that can be used to generate the pdf graphs
*** '''''*/SAMPLE.qplot.R'' - Rscript that can be used to generate the pdf graphs'''
*** '''*.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 *recab* sub-pipeline failed.
