############### Example usage ############### Below are several examples of basic bedtools usage. Example BED files are provided in the /data directory of the bedtools distribution. ========================================================================== bedtools intersect ========================================================================== Report the base-pair overlap between sequence alignments and genes. .. code-block:: bash bedtools intersect -a reads.bed -b genes.bed Report whether each alignment overlaps one or more genes. If not, the alignment is not reported. .. code-block:: bash bedtools intersect -a reads.bed -b genes.bed -u Report those alignments that overlap NO genes. Like "grep -v" .. code-block:: bash bedtools intersect -a reads.bed -b genes.bed -v Report the number of genes that each alignment overlaps. .. code-block:: bash bedtools intersect -a reads.bed -b genes.bed -c Report the entire, original alignment entry for each overlap with a gene. .. code-block:: bash bedtools intersect -a reads.bed -b genes.bed -wa Report the entire, original gene entry for each overlap with a gene. .. code-block:: bash bedtools intersect -a reads.bed -b genes.bed -wb Report the entire, original alignment and gene entries for each overlap. .. code-block:: bash 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. .. code-block:: bash bedtools intersect -a exons.bed -b repeatMasker.bed -f 0.50 Only 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. .. code-block:: bash bedtools intersect -a SV.bed -b segmentalDups.bed -f 0.50 -r Read BED A from stdin. For example, find genes that overlap LINEs but not SINEs. .. code-block:: bash bedtools intersect -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed -v Retain only single-end BAM alignments that overlap exons. .. code-block:: bash bedtools intersect -abam reads.bam -b exons.bed > reads.touchingExons.bam Retain only single-end BAM alignments that do not overlap simple sequence repeats. .. code-block:: bash bedtools intersect -abam reads.bam -b SSRs.bed -v > reads.noSSRs.bam ========================================================================== bedtools bamtobed ========================================================================== Convert BAM alignments to BED format. .. code-block:: bash bedtools bamtobed -i reads.bam > reads.bed Convert BAM alignments to BED format using the BAM edit distance (NM) as the BED "score". .. code-block:: bash bedtools bamtobed -i reads.bam -ed > reads.bed Convert BAM alignments to BEDPE format. .. code-block:: bash bedtools bamtobed -i reads.bam -bedpe > reads.bedpe ========================================================================== bedtools window ========================================================================== Report all genes that are within 10000 bp upstream or downstream of CNVs. .. code-block:: bash bedtools window -a CNVs.bed -b genes.bed -w 10000 Report all genes that are within 10000 bp upstream or 5000 bp downstream of CNVs. .. code-block:: bash 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. .. code-block:: bash 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 overlapping features to be the closest. Find the closest ALU to each gene. .. code-block:: bash 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 a tie. .. code-block:: bash 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 a tie. .. code-block:: bash 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. .. code-block:: bash bedtools subtract -a genes.bed -b introns.bed ========================================================================== bedtools merge ========================================================================== .. note:: ``merge`` requires that the input is sorted by chromosome and then by start coordinate. For example, for BED files, one would first sort the input as follows: ``sort -k1,1 -k2,2n input.bed > input.sorted.bed`` Merge overlapping repetitive elements into a single entry. .. code-block:: bash bedtools merge -i repeatMasker.bed Merge overlapping repetitive elements into a single entry, returning the number of entries merged. .. code-block:: bash bedtools merge -i repeatMasker.bed -n Merge nearby (within 1000 bp) repetitive elements into a single entry. .. code-block:: bash bedtools merge -i repeatMasker.bed -d 1000 ========================================================================== bedtools coverage ========================================================================== Compute the coverage of aligned sequences on 10 kilobase "windows" spanning the genome. .. code-block:: bash bedtools coverage -a reads.bed -b windows10kb.bed | head chr1 0 10000 0 10000 0.00 chr1 10001 20000 33 10000 0.21 chr1 20001 30000 42 10000 0.29 chr1 30001 40000 71 10000 0.36 Compute the coverage of aligned sequences on 10 kilobase "windows" spanning the genome and created a BEDGRAPH of the number of aligned reads in each window for display on the UCSC browser. .. code-block:: bash 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 the genome and created a BEDGRAPH of the fraction of each window covered by at least one aligned read for display on the UCSC browser. .. code-block:: bash 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 repetitive elements. .. code-block:: bash bedtools complement -i repeatMasker.bed -g hg18.genome ========================================================================== bedtools shuffle ========================================================================== Randomly place all discovered variants in the genome. However, prevent them from being placed in know genome gaps. .. code-block:: bash bedtools shuffle -i variants.bed -g hg18.genome -excl genome_gaps.bed Randomly place all discovered variants in the genome. However, prevent them from being placed in know genome gaps and require that the variants be randomly placed on the same chromosome. .. code-block:: bash bedtools shuffle -i variants.bed -g hg18.genome -excl genome_gaps.bed -chrom