Changes

* '''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

*** *.genoCheck.depthRG - depth distribution of the sequence reads per read group

*** */SAMPLE.genoCheck.depthRG - depth distribution of the sequence reads per read group

*** *.genoCheck.depthSM - depth distribution of the sequence reads per sample

*** */SAMPLE.genoCheck.depthSM - depth distribution of the sequence reads per sample

*** ''*.genoCheck.done'' - temp file indicating this step completed successfully

*** ''*/SAMPLE.genoCheck.OK'' - temp file indicating the VerifyBAMID step completed successfully

*** *.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

*** '''*.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