Man pages for PhanstielLab/bedtoolsr
Bedtools Wrapper

bt.annotateAnnotates the depth & breadth of coverage of features from...
bt.bamtobedConverts BAM alignments to BED6 or BEDPE format.
bt.bamtofastqConvert BAM alignments to FASTQ files.
bt.bed12tobed6Splits BED12 features into discrete BED6 features.
bt.bedpetobamConverts feature records to BAM format.
bt.bedtobamConverts feature records to BAM format.
bt.closestFor each feature in A, finds the closest feature (upstream or...
bt.clusterClusters overlapping/nearby BED/GFF/VCF intervals.
bt.complementReturns the base pair complement of a feature file.
bt.coverageReturns the depth and breadth of coverage of features from B...
bt.expandReplicate lines in a file based on columns of comma-separated...
bt.fisherCalculate Fisher statistic b/w two feature files.
bt.flankCreates flanking interval(s) for each BED/GFF/VCF feature.
bt.genomecovCompute the coverage of a feature file among a genome.
bt.getfastaExtract DNA sequences from a fasta file based on feature...
bt.groupbySummarizes a dataset column based upon common column...
bt.igvCreates a batch script to create IGV images at each interval...
bt.intersectReport overlaps between two feature files.
bt.jaccardCalculate Jaccard statistic b/w two feature files. Jaccard is...
bt.linksCreates HTML links to an UCSC Genome Browser from a feature...
bt.makewindowsMakes adjacent or sliding windows across a genome or BED...
bt.mapApply a function to a column from B intervals that overlap A.
bt.maskfastaMask a fasta file based on feature coordinates.
bt.mergeMerges overlapping BED/GFF/VCF entries into a single...
bt.multicovCounts sequence coverage for multiple bams at specific loci.
bt.multiinterIdentifies common intervals among multiple BED/GFF/VCF files.
bt.nucProfiles the nucleotide content of intervals in a fasta file.
bt.overlapComputes the amount of overlap (positive values) or distance...
bt.pairtobedReport overlaps between a BEDPE file and a BED/GFF/VCF file.
bt.pairtopairReport overlaps between two paired-end BED files (BEDPE).
bt.randomGenerate random intervals among a genome.
bt.reldistCalculate the relative distance distribution b/w two feature...
bt.sampleTake sample of input file(s) using reservoir sampling...
bt.shiftShift each feature by requested number of base pairs.
bt.shuffleRandomly permute the locations of a feature file among a...
bt.slopAdd requested base pairs of "slop" to each feature.
bt.sortSorts a feature file in various and useful ways.
bt.spacingReport (last col.) the gap lengths between intervals in a...
bt.splitSplit a Bed file.
bt.subtractRemoves the portion(s) of an interval that is overlapped by...
bt.tagAnnotates a BAM file based on overlaps with multiple...
bt.unionbedgCombines multiple BedGraph files into a single file, allowing...
bt.windowExamines a "window" around each feature in A and reports all...
createOptionsCreates options based on user input
deleteTempFilesDeletes temp files
establishPathsDetermines if arguments are paths or R objects. Makes temp...
PhanstielLab/bedtoolsr documentation built on May 14, 2019, 9:37 a.m.