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Revision as of 10:04, 23 October 2014
, 10:04, 23 October 2014→Alignment Pipeline Output
**** 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
*** ''*.qplot.done'' - temp file indicating this step completed successfully
*** '''*.qplot.R''' - Rscript that can be used to generate the pdf graphs
*** '''*.qplot.R''' - Rscript that can be used to generate the pdf graphs
