Changes

The final BAM files produced by the alignment pipeline are:

The final BAM files produced by the alignment pipeline are:

  ls $GCOUT/alignment.recal/*.recal.bam

  ls $GCOUT/alignment.recal/*.recal.bam $GCOUT/alignment.recal/*.recal.bam.bai

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 $GCOUT/QCFiles/*.genoCheck.selfRG $GCOUT/QCFiles/*.genoCheck.selfSM

  ls $GCOUT/QCFiles/*.genoCheck.self* $GCOUT/QCFiles/*.genoCheck.depth*

[[Understanding VerifyBamID output]]

[[Understanding VerifyBamID output]]