Below are several examples of basic bedtools usage. Example BED files areprovided in the /data directory of the bedtools distribution.
bedtools intersect¶
Report the base-pair overlap between sequence alignments and genes.
bedtools intersect -a reads.bed -b genes.bed
Report whether each alignment overlaps one or more genes. If not, the alignment is not reported.
bedtools intersect -a reads.bed -b genes.bed -u
Report those alignments that overlap NO genes. Like “grep -v”
bedtools intersect -a reads.bed -b genes.bed -v
Report the number of genes that each alignment overlaps.
bedtools intersect -a reads.bed -b genes.bed -c
Report the entire, original alignment entry for each overlap with a gene.
bedtools intersect -a reads.bed -b genes.bed -wa
Report the entire, original gene entry for each overlap with a gene.
bedtools intersect -a reads.bed -b genes.bed -wb
Report the entire, original alignment and gene entries for each overlap.
bedtools intersect -a reads.bed -b genes.bed -wa -wb
Only report an overlap with a repeat if it spans at least 50% of the exon.
bedtools intersect -a exons.bed -b repeatMasker.bed -f 0.50Only report an overlap if comprises 50% of the structural variant and 50% of the segmental duplication. Thus, it is reciprocally at least a 50% overlap.
bedtools intersect -a SV.bed -b segmentalDups.bed -f 0.50 -rRead BED A from stdin. For example, find genes that overlap LINEs but not SINEs.
bedtools intersect -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed -vRetain only single-end BAM alignments that overlap exons.
bedtools intersect -abam reads.bam -b exons.bed > reads.touchingExons.bam
Retain only single-end BAM alignments that do not overlap simple sequencerepeats.
bedtools intersect -abam reads.bam -b SSRs.bed -v > reads.noSSRs.bam
bedtools bamtobed¶
Convert BAM alignments to BED format.
bedtools bamtobed -i reads.bam > reads.bed
Convert BAM alignments to BED format using the BAM edit distance (NM) as theBED “score”.
bedtools bamtobed -i reads.bam -ed > reads.bed
Convert BAM alignments to BEDPE format.
bedtools bamtobed -i reads.bam -bedpe > reads.bedpe
bedtools window¶
Report all genes that are within 10000 bp upstream or downstream of CNVs.
bedtools window -a CNVs.bed -b genes.bed -w 10000Report all genes that are within 10000 bp upstream or 5000 bp downstream ofCNVs.
bedtools window -a CNVs.bed -b genes.bed -l 10000 -r 5000
Report all SNPs that are within 5000 bp upstream or 1000 bp downstream of genes.Define upstream and downstream based on strand.
bedtools window -a genes.bed -b snps.bed -l 5000 -r 1000 -sw
bedtools closest¶
Note: By default, if there is a tie for closest, all ties will be reported. closestBed allows overlappingfeatures to be the closest.
Find the closest ALU to each gene.
bedtools closest -a genes.bed -b ALUs.bed
Find the closest ALU to each gene, choosing the first ALU in the file if there is atie.
bedtools closest -a genes.bed -b ALUs.bed -t first
Find the closest ALU to each gene, choosing the last ALU in the file if there is atie.
bedtools closest -a genes.bed -b ALUs.bed -t last
bedtools subtract¶
Note
If a feature in A is entirely “spanned” by any feature in B, it will not be reported.
Remove introns from gene features. Exons will (should) be reported.
bedtools subtract -a genes.bed -b introns.bed
bedtools merge¶
Note
merge requires that the input is sorted by chromosome and then by startcoordinate. For example, for BED files, one would first sort the inputas follows: sort -k1,1 -k2,2n input.bed > input.sorted.bed
Merge overlapping repetitive elements into a single entry.
bedtools merge -i repeatMasker.bed
Merge overlapping repetitive elements into a single entry, returning the number ofentries merged.
bedtools merge -i repeatMasker.bed -n
Merge nearby (within 1000 bp) repetitive elements into a single entry.
bedtools merge -i repeatMasker.bed -d 1000bedtools coverage¶
Compute the coverage of aligned sequences on 10 kilobase “windows” spanning thegenome.
bedtools coverage -a reads.bed -b windows10kb.bed | headchr1 0 10000 0 10000 0.00chr1 10001 20000 33 10000 0.21chr1 20001 30000 42 10000 0.29chr1 30001 40000 71 10000 0.36
Compute the coverage of aligned sequences on 10 kilobase “windows” spanning thegenome and created a BEDGRAPH of the number of aligned reads in each window fordisplay on the UCSC browser.
bedtools coverage -a reads.bed -b windows10kb.bed | cut -f 1-4 > windows10kb.cov.bedg
Compute the coverage of aligned sequences on 10 kilobase “windows” spanning thegenome and created a BEDGRAPH of the fraction of each window covered by at leastone aligned read for display on the UCSC browser.
bedtools coverage -a reads.bed -b windows10kb.bed | \ awk '{OFS="\t"; print $1,$2,$3,$6}' \ > windows10kb.pctcov.bedg
bedtools complement¶
Report all intervals in the human genome that are not covered by repetitiveelements.
bedtools complement -i repeatMasker.bed -g hg18.genome
bedtools shuffle¶
Randomly place all discovered variants in the genome. However, prevent themfrom being placed in know genome gaps.
bedtools shuffle -i variants.bed -g hg18.genome -excl genome_gaps.bed
Randomly place all discovered variants in the genome. However, prevent themfrom being placed in know genome gaps and require that the variants be randomlyplaced on the same chromosome.
bedtools shuffle -i variants.bed -g hg18.genome -excl genome_gaps.bed -chrom
