############### Advanced usage ############### ========================================================================== Mask all regions in a genome except for targeted capture regions. ========================================================================== Step 1. Add 500 bp up and downstream of each probe .. code-block:: bash bedtools slop -i probes.bed -g hg18.genome -b 500 > probes.500bp.bed NB genome is two column chromosome size list - i.e. https://genome.ucsc.edu/goldenpath/help/hg18.chrom.sizes Step 2. Get a BED file of all regions not covered by the probes (+500 bp up/down) .. code-block:: bash bedtools complement -i probes.500bp.bed -g hg18.genome > probes.500bp.complement.bed Step 3. Create a masked genome where all bases are masked except for the probes +500bp .. code-block:: bash bedtools maskfasta -fi hg18.fa -bed probes.500bp.complement.bed \ -fo hg18.probecomplement.masked.fa ========================================================================== Screening for novel SNPs. ========================================================================== Find all SNPs that are not in dbSnp and not in the latest 1000 genomes calls .. code-block:: bash bedtools intersect -a snp.calls.bed -b dbSnp.bed -v | \ bedtools intersect -a - -b 1KG.bed -v | \ > snp.calls.novel.bed ========================================================================== Computing the coverage of features that align entirely within an interval. ========================================================================== By default, bedtools ``coverage`` counts any feature in A that overlaps B by >= 1 bp. If you want to require that a feature align entirely within B for it to be counted, you can first use intersectBed with the "-f 1.0" option. .. code-block:: bash bedtools intersect -a features.bed -b windows.bed -f 1.0 | \ bedtools coverage -a windows.bed -b - \ > windows.bed.coverage ========================================================================== Computing the coverage of BAM alignments on exons. ========================================================================== One can combine ``samtools`` with ``bedtools`` to compute coverage directly from the BAM data by using ``bamtobed``. .. code-block:: bash bedtools bamtobed -i reads.bam | \ bedtools coverage -a exons.bed -b - \ > exons.bed.coverage Take it a step further and require that coverage be from properly-paired reads. .. code-block:: bash samtools view -uf 0x2 reads.bam | \ coverageBed -abam - -b exons.bed \ > exons.bed.proper.coverage ========================================================================== Computing coverage separately for each strand. ========================================================================== Use grep to only look at forward strand features (i.e. those that end in "+"). .. code-block:: bash bedtools bamtobed -i reads.bam | \ grep \+$ | \ bedtools coverage -a - -b genes.bed \ > genes.bed.forward.coverage Use grep to only look at reverse strand features (i.e. those that end in "-"). .. code-block:: bash bedtools bamtobed -i reads.bam | \ grep \-$ | \ bedtools coverage -a - -b genes.bed \ > genes.bed.reverse.coverage