From 20244ad9a9a2c3313dd90851e9d87d41f805cf42 Mon Sep 17 00:00:00 2001 From: Aaron <aaronquinlan@gmail.com> Date: Mon, 14 Jan 2013 23:24:51 -0500 Subject: [PATCH] [DOCS] update adv usage. --- docs/content/advanced-usage.rst | 129 +++++++++++++++++--------------- 1 file changed, 69 insertions(+), 60 deletions(-) diff --git a/docs/content/advanced-usage.rst b/docs/content/advanced-usage.rst index 8f706807..e748b3ff 100755 --- a/docs/content/advanced-usage.rst +++ b/docs/content/advanced-usage.rst @@ -4,89 +4,98 @@ Advanced usage ========================================================================== -7.1 Mask all regions in a genome except for targeted capture regions. +Mask all regions in a genome except for targeted capture regions. ========================================================================== -# Add 500 bp up and downstream of each probe -:: - slopBed -i probes.bed -b 500 > probes.500bp.bed + +Step 1. Add 500 bp up and downstream of each probe + +.. code-block:: bash + + bedtools slop -i probes.bed -b 500 > probes.500bp.bed -# Get a BED file of all regions not covered by the probes (+500 bp up/down) -:: - complementBed -i probes.500bp.bed -g hg18.genome > probes.500bp.complement.bed +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 -# Create a masked genome where all bases are masked except for the probes +500bp -:: - maskFastaFromBed -in hg18.fa -bed probes.500bp.complement.bed -fo hg18.probecomplement. - masked.fa + +Step 3. Create a masked genome where all bases are masked except for the probes +500bp + +.. code-block:: bash + + bedtools maskfasta -in hg18.fa -bed probes.500bp.complement.bed -fo \ + > hg18.probecomplement.masked.fa ========================================================================== -7.2 Screening for novel SNPs. +Screening for novel SNPs. ========================================================================== -# Find all SNPs that are not in dbSnp and not in the latest 1000 genomes calls -:: - intersectBed -a snp.calls.bed -b dbSnp.bed -v | intersectBed -a stdin -b 1KG.bed - -v > snp.calls.novel.bed +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 ========================================================================== -7.3 Computing the coverage of features that align entirely within an -interval. +Computing the coverage of features that align entirely within an interval. ========================================================================== -# By default, coverageBed 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. -:: - intersectBed -a features.bed -b windows.bed -f 1.0 | coverageBed -a stdin -b - windows.bed > windows.bed.coverage + +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 - -b \ + > windows.bed.coverage ========================================================================== -7.4 Computing the coverage of BAM alignments on exons. +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. -:: - bamToBed -i reads.bam | coverageBed -a stdin -b exons.bed > exons.bed.coverage +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 - -b exons.bed \ + > exons.bed.coverage -# Take it a step further and require that coverage be from properly-paired reads. -:: - samtools view -bf 0x2 reads.bam | bamToBed -i stdin | coverageBed -a stdin -b - exons.bed > exons.bed.proper.coverage +Take it a step further and require that coverage be from properly-paired reads. +.. code-block:: bash -========================================================================== -7.5 Computing coverage separately for each strand. -========================================================================== -# Use grep to only look at forward strand features (i.e. those that end in "+"). -:: - bamToBed -i reads.bam | grep \+$ | coverageBed -a stdin -b genes.bed > - genes.bed.forward.coverage + samtools view -uf 0x2 reads.bam | \ + coverageBed -abam - -b exons.bed \ + > exons.bed.proper.coverage -# Use grep to only look at reverse strand features (i.e. those that end in "-"). -:: - bamToBed -i reads.bam | grep \-$ | coverageBed -a stdin -b genes.bed > - genes.bed.forward.coverage - ========================================================================== -7.6 Find structural variant calls that are private to one sample. +Computing coverage separately for each strand. ========================================================================== -# : -:: - pairToPair -a sample1.sv.bedpe -b othersamples.sv.bedpe -type neither > - sample1.sv.private.bedpe - - +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 -================================================================================== -7.7 Exclude SV deletions that appear to be ALU insertions in the reference genome. -================================================================================== -# We'll require that 90% of the inner span of the deletion be overlapped by a -recent ALU. -:: - pairToBed -a deletions.sv.bedpe -b ALUs.recent.bed -type notispan -f 0.80 > - deletions.notALUsinRef.bedpe \ No newline at end of file -- GitLab