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Revision as of 23:08, 7 December 2014
, 23:08, 7 December 2014→Quality Control Output
''We may hold off on reviewing this until Friday.''
''We may hold off on reviewing this until Friday.''
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ls QCFiles/
Check QC directory
ls QCFiles/
Check for Sample Contamination:
less -S QCFiles/Sample*.genoCheck.selfSM
Look for FREEMIX column. OR notice that it is column 7:
cut -f7 QCFiles/Sample*.genoCheck.selfSM
Look at QPLOT stats:
less QCFiles/Sample*.qplot.stats
* What is your Mapping Rate%?
* What is your MeanDepth?
* What is your GenomeCover(%)?
Let's generate the plots:
* R script will create PDF
** automatically set PDF path to full path where the R script is
*** That wouldn't work since I didn't align in your directory & instead moved the files in there afterwards
*** I hand modified it to relative directory from your home directory, so you need to move to your home directory to create the PDF
cd
Rscript Sample*/output/QCFiles/Sample*.qplot.R
evince Sample*/output/QCFiles/Sample*.qplot.pdf&
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