Man pages for mskilab/bamUtils
Utility functions for manipulating BAMs

bam.cov.grGet coverage as GRanges from BAM on custom set of GRanges
bam.cov.tileGet coverage as GRanges from BAM on genome tiles across...
bamflagReturns matrix of bits from BAM flags
bamtagOutputs a tag to identify duplicate reads in GRanges input
chunkchunk
countCigarCount bases in cigar string
count.clipsReturn data.frame with fields of "right" soft clips and...
get.mate.grreturns GRanges corresponding to mates of reads
get.pairs.grlGet coverage as GRanges from BAM on custom set of GRanges
is.paired.endCheck if BAM file is paired end by using 0x1 flag
mafcountWrapper around varcount adapted to tumor and normal "paired"...
read.bamRead BAM file into GRanges or data.table
splice.cigarGet coverage as GRanges from BAM on custom set of GRanges
varbaseReturns variant bases and ranges from GRanges or...
varcountWrapper around applyPileups
mskilab/bamUtils documentation built on July 10, 2018, 8:43 a.m.