| 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 |
| identifyIlluminaReadGroups |
Reassigning read groups based on the platform unit in their name |
| liftOver |
Lifting GERP scores from one reference to another |
| 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 |