Chapter 4 Read tasks
assessSoftClipping | Assessing level of soft clipping in BAM file |
BAMDiagnostics | Estimating depth and read property frequencies |
downsample | Downsampling a BAM file |
filterBAM | Writing reads that pass filters to BAM file |
mergeOverlappingReads | Merging paired-end reads in BAM file |
mergeRG | Merging read groups in a BAM file |
PMDS | Filtering for ancient reads using PMDS |
qualityTransformation | Printing Quality Transformation |
trimSoftClips | Removing soft clipped bases from reads |