6
==========================================================================
7
7.1 Mask all regions in a genome except for targeted capture regions.
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==========================================================================
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# Add 500 bp up and downstream of each probe
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slopBed -i probes.bed -b 500 > probes.500bp.bed
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# Get a BED file of all regions not covered by the probes (+500 bp up/down)
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complementBed -i probes.500bp.bed -g hg18.genome > probes.500bp.complement.bed
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# Create a masked genome where all bases are masked except for the probes +500bp
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maskFastaFromBed -in hg18.fa -bed probes.500bp.complement.bed -fo hg18.probecomplement.
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==========================================================================
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7.2 Screening for novel SNPs.
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==========================================================================
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# Find all SNPs that are not in dbSnp and not in the latest 1000 genomes calls
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intersectBed -a snp.calls.bed -b dbSnp.bed -v | intersectBed -a stdin -b 1KG.bed
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-v > snp.calls.novel.bed
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==========================================================================
34
7.3 Computing the coverage of features that align entirely within an
36
==========================================================================
37
# By default, coverageBed counts any feature in A that overlaps B by >= 1 bp. If
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you want to require that a feature align entirely within B for it to be counted,
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you can first use intersectBed with the "-f 1.0" option.
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intersectBed -a features.bed -b windows.bed -f 1.0 | coverageBed -a stdin -b
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windows.bed > windows.bed.coverage
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==========================================================================
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7.4 Computing the coverage of BAM alignments on exons.
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==========================================================================
48
# One can combine SAMtools with BEDtools to compute coverage directly from the BAM
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data by using bamToBed.
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bamToBed -i reads.bam | coverageBed -a stdin -b exons.bed > exons.bed.coverage
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# Take it a step further and require that coverage be from properly-paired reads.
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samtools view -bf 0x2 reads.bam | bamToBed -i stdin | coverageBed -a stdin -b
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exons.bed > exons.bed.proper.coverage
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==========================================================================
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7.5 Computing coverage separately for each strand.
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==========================================================================
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# Use grep to only look at forward strand features (i.e. those that end in "+").
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bamToBed -i reads.bam | grep \+$ | coverageBed -a stdin -b genes.bed >
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genes.bed.forward.coverage
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# Use grep to only look at reverse strand features (i.e. those that end in "-").
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bamToBed -i reads.bam | grep \-$ | coverageBed -a stdin -b genes.bed >
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genes.bed.forward.coverage
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==========================================================================
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7.6 Find structural variant calls that are private to one sample.
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==========================================================================
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pairToPair -a sample1.sv.bedpe -b othersamples.sv.bedpe -type neither >
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sample1.sv.private.bedpe
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==================================================================================
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7.7 Exclude SV deletions that appear to be ALU insertions in the reference genome.
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==================================================================================
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# We'll require that 90% of the inner span of the deletion be overlapped by a
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pairToBed -a deletions.sv.bedpe -b ALUs.recent.bed -type notispan -f 0.80 >
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deletions.notALUsinRef.bedpe
b'\\ No newline at end of file'
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docs/content/advanced-usage.rst
