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BEDTools

bio.toolsVerified30 docs · 15.9K tokens
v2.31.1

Swiss-army knife of genome feature analysis toolset

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1###############
2Advanced usage
3###############
4

5

6==========================================================================
7Mask all regions in a genome except for targeted capture regions.
8==========================================================================
9

10Step 1. Add 500 bp up and downstream of each probe
11

12.. code-block:: bash
13

14  bedtools slop -i probes.bed -g hg18.genome -b 500 > probes.500bp.bed
15  
16NB genome is two column chromosome size list - i.e. https://genome.ucsc.edu/goldenpath/help/hg18.chrom.sizes
17

18Step 2. Get a BED file of all regions not covered by the probes (+500 bp up/down)
19

20

21.. code-block:: bash
22

23  bedtools complement -i probes.500bp.bed -g hg18.genome > probes.500bp.complement.bed
24  
25

26Step 3. Create a masked genome where all bases are masked except for the probes +500bp
27

28.. code-block:: bash
29

30  bedtools maskfasta -fi hg18.fa -bed probes.500bp.complement.bed \
31  -fo hg18.probecomplement.masked.fa
32

33

34

35==========================================================================
36Screening for novel SNPs.
37==========================================================================
38Find all SNPs that are not in dbSnp and not in the latest 1000 genomes calls
39

40.. code-block:: bash
41

42  bedtools intersect -a snp.calls.bed -b dbSnp.bed -v | \ 
43  bedtools intersect -a - -b 1KG.bed -v | \
44  > snp.calls.novel.bed
45

46

47==========================================================================
48Computing the coverage of features that align entirely within an interval.
49==========================================================================
50

51By default, bedtools ``coverage`` counts any feature in A that overlaps B 
52by >= 1 bp. If you want to require that a feature align entirely within B for 
53it to be counted, you can first use intersectBed with the "-f 1.0" option.
54

55.. code-block:: bash
56

57  bedtools intersect -a features.bed -b windows.bed -f 1.0 | \
58  bedtools coverage -a windows.bed -b - \
59  > windows.bed.coverage
60

61

62==========================================================================
63Computing the coverage of BAM alignments on exons.
64==========================================================================
65One can combine ``samtools`` with ``bedtools`` to compute coverage directly 
66from the BAM data by using ``bamtobed``.
67

68.. code-block:: bash
69

70  bedtools bamtobed -i reads.bam | \
71  bedtools coverage -a exons.bed -b - \
72  > exons.bed.coverage
73  
74

75Take it a step further and require that coverage be from properly-paired reads.
76

77.. code-block:: bash
78

79  samtools view -uf 0x2 reads.bam | \
80  coverageBed -abam - -b exons.bed \
81  > exons.bed.proper.coverage
82

83

84

85==========================================================================
86Computing coverage separately for each strand.
87==========================================================================
88Use grep to only look at forward strand features (i.e. those that end in "+").
89

90.. code-block:: bash
91

92  bedtools bamtobed -i reads.bam | \
93  grep \+$  | \
94  bedtools coverage -a - -b genes.bed \
95  > genes.bed.forward.coverage
96

97Use grep to only look at reverse strand features (i.e. those that end in "-").
98

99.. code-block:: bash
100

101  bedtools bamtobed -i reads.bam | \
102  grep \-$ | \
103  bedtools coverage -a - -b genes.bed \
104  > genes.bed.reverse.coverage
Source

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Installation

conda
conda install -c bioconda bedtools

Container Images

quay.io
docker pull quay.io/bedtools:2.31.1--hf5e1c6e_1

Version History

  • v2.31.1