Man pages for mskilab/bamUtils
Utility functions for manipulating BAMs
| bam.cov.gr | Get coverage as GRanges from BAM on custom set of GRanges |
| bam.cov.tile | Get coverage as GRanges from BAM on genome tiles across... |
| bamflag | Returns matrix of bits from BAM flags |
| bamorcram | bamorcram |
| bamtag | Outputs a tag to identify duplicate reads in GRanges input |
| chunk | chunk |
| countCigar | Count bases in cigar string |
| count.clips | Return data.frame with fields of "right" soft clips and... |
| get.mate.gr | returns GRanges corresponding to mates of reads |
| get.pairs.grl | Get coverage as GRanges from BAM on custom set of GRanges |
| is.paired.end | Check if BAM file is paired end by using 0x1 flag |
| mafcount | Wrapper around varcount adapted to tumor and normal "paired"... |
| read.bam | Read BAM file into GRanges or data.table |
| splice.cigar | Get coverage as GRanges from BAM on custom set of GRanges |
| varbase | Returns variant bases and ranges from GRanges or... |
| varcount | Wrapper around applyPileups |
