Advanced usage

Mask all regions in a genome except for targeted capture regions.

Step 1. Add 500 bp up and downstream of each probe

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)

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

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

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.

bedtools intersect -a features.bed -b windows.bed -f 1.0 | \
bedtools coverage -a - -b windows.bed \
> 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.

bedtools bamtobed -i reads.bam | \
bedtools coverage -a - -b exons.bed \
> exons.bed.coverage

Take it a step further and require that coverage be from properly-paired reads.

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 “+”).

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 “-”).

bedtools bamtobed -i reads.bam | \
grep \-$ | \
bedtools coverage -a - -b genes.bed \
> genes.bed.reverse.coverage
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