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bedtools shuffle bedtools shuffle [OPTIONS] -i -g bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” BED/GFF/VCF file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another. Show
bedtools bamtofastq bedtools bamtofastq [OPTIONS] -i -fq bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format. Show
bedtools intersect bedtools intersect [OPTIONS] -a \ -b By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both BED/GFF/VCF and BAM files as input. Show
bedtools bamtobed bedtools bamtobed [OPTIONS] -i bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. Show
bedtools cluster bedtools cluster [OPTIONS] -i Similar to merge, cluster report each set of overlapping or “book-ended” features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined. Show
bedtools coverage bedtools coverage [OPTIONS] -a \ -b The bedtools coverage tool computes both the depth and breadth of coverage of features in file B on the features in file A. For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. One advantage that bedtools coverage offers is that it not only counts the number of features that overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus, bedtools coverage also computes the breadth of coverage observed for each interval in A. Show
bedtools slop bedtools slop [OPTIONS] -i -g [-b or (-l and -r)] bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-,$3+}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end > chromosome size). Show
bedtools complement bedtools complement -i -g bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. Show
genomeCoverageBed genomeCoverageBed [OPTIONS] [-i|-ibam] -g (iff. -i) bedtools genomecov computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. Show
bedtools genomecov bedtools genomecov [OPTIONS] [-i|-ibam] -g (iff. -i) bedtools genomecov computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. Show
bedtools annotate bedtools annotate [OPTIONS] -i -files FILE1 FILE2 FILE3 ... FILEn bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command. Show
bedtools flank bedtools flank [OPTIONS] -i -g [-b or (-l and -r)] bedtools flank will create two new flanking intervals for each interval in a BED/GFF/VCF file. Note that flank will restrict the created flanking intervals to the size of the chromosome (i.e. no start < 0 and no end > chromosome size). Show
coverageBed coverageBed [OPTIONS] -a \ -b The bedtools coverage tool computes both the depth and breadth of coverage of features in file B on the features in file A. For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. One advantage that bedtools coverage offers is that it not only counts the number of features that overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus, bedtools coverage also computes the breadth of coverage observed for each interval in A. Show
bamToBed bamToBed [OPTIONS] -i bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. Show
clusterBed clusterBed [OPTIONS] -i Similar to merge, cluster report each set of overlapping or “book-ended” features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined. Show
bedtools subtract bedtools subtract [OPTIONS] -a -b bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported. Show
bamToFastq bamToFastq [OPTIONS] -i -fq bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format. Show
annotateBed annotateBed [OPTIONS] -i -files FILE1 FILE2 FILE3 ... FILEn bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command. Show
complementBed -i complementBed -i -g bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. Show
GEMINI annotate gemini load -v my.vcf -t snpEff my.db It is inevitable that researchers will want to enhance the GEMINI framework with their own, custom annotations. GEMINI provides a sub-command called annotate for exactly this purpose. Show