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The final BAM files produced by the mapping pipeline are:
The final BAM files produced by the mapping pipeline are:
ls mappingResults/alignment.recal/*.recal.bam
ls $GCOUT/alignment.recal/*.recal.bam
Index files (.bai) for these BAMs are also in that directory.
Index files (.bai) for these BAMs are also in that directory.
The QC files for verifyBamID are:
The QC files for verifyBamID are:
ls mappingResults/QCFiles/*.genoCheck.selfRG mappingResults/QCFiles/*.genoCheck.selfSM
ls $GCOUT/QCFiles/*.genoCheck.selfRG $GCOUT/QCFiles/*.genoCheck.selfSM
[[Understanding VerifyBamID output]]
[[Understanding VerifyBamID output]]
The QC files for qplot are:
The QC files for qplot are:
ls mappingResults/QCFiles/*.qplot.R mappingResults/QCFiles/*.qplot.stats
ls $GCOUT/QCFiles/*.qplot.R $GCOUT/QCFiles/*.qplot.stats
[[Understanding QPLOT output]]
[[Understanding QPLOT output]]
Run the variant calling pipeline:
Run the variant calling pipeline:
$GCHOME/gotcloud snpcall --conf [[GBR60vc.conf]] --outdir vcResults --snpcall --numjobs 2
TBD - maybe merge both mapping & umake into a single script and have them as options.
TBD - maybe merge both mapping & umake into a single script and have them as options.
