### Install Bedtools using Apt-Get (Debian/Ubuntu)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/installation

This command installs the Bedtools package using the 'apt-get' package manager, prevalent in Debian, Ubuntu, and their derivatives. Administrator privileges may be required.

```bash
apt-get install bedtools
```

--------------------------------

### Install Bedtools Binary on Linux

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/installation

This snippet demonstrates how to download and make executable a pre-compiled static binary of Bedtools on Linux systems. It assumes the user has wget or curl available and read access to the GitHub releases page.

```bash
mv bedtools.static.binary bedtools
chmod a+x bedtools
```

--------------------------------

### Compile Bedtools from Source (GitHub)

Source: https://bedtools.readthedocs.io/en/latest/content/installation

Instructions for downloading the bedtools source code from GitHub, extracting it, and compiling it using `make`. This method is intended for UNIX or OS X and requires the GCC compiler. The compiled binaries will be available in the `./bin/` directory.

```bash
$ wget https://github.com/arq5x/bedtools2/releases/download/v2.29.1/bedtools-2.29.1.tar.gz
$ tar -zxvf bedtools-2.29.1.tar.gz
$ cd bedtools2
$ make
```

--------------------------------

### Install Bedtools using Homebrew (OSX)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/installation

This sequence of commands installs Bedtools on macOS using the Homebrew package manager. It first taps the 'science' repository and then installs the bedtools package. Administrator privileges are typically not required for user-level installations.

```bash
brew tap homebrew/science
brew install bedtools
```

--------------------------------

### Install bedtools using curl and make

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/quick-start

This snippet shows how to download, extract, compile, and install bedtools from a tarball using curl and the make command. It assumes you have the necessary build tools installed.

```bash
curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz
tar -zxvf BEDTools.tar.gz
cd BEDTools
make
sudo cp bin/* /usr/local/bin/
```

--------------------------------

### Sorting BED File Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/fisher

An example of how to sort a BED file by start position, which is a common preprocessing step for genomic interval analysis tools like bedtools.

```bash
sort -k1,1 -k2,2n in.bed > in.sorted.bed
```

--------------------------------

### Compile Bedtools from Source via GitHub

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/installation

This code block shows the steps to download, extract, and compile Bedtools from its source code available on GitHub. It requires wget for downloading the tarball, tar for extraction, and make for compilation. The GCC compiler is assumed to be available.

```bash
wget https://github.com/arq5x/bedtools2/releases/download/v2.29.1/bedtools-2.29.1.tar.gz 
tar -zxvf bedtools-2.29.1.tar.gz
cd bedtools2
make
```

--------------------------------

### Install Bedtools using MacPorts (OSX)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/installation

This command installs Bedtools on macOS using the MacPorts package management system. Administrator privileges may be required.

```bash
port install bedtools
```

--------------------------------

### Install Bedtools using Yum (Fedora/CentOS)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/installation

This command installs the Bedtools package using the 'yum' package manager, commonly found on Fedora, CentOS, and related Linux distributions. Administrator privileges may be required.

```bash
yum install BEDTools
```

--------------------------------

### Clone Bedtools Development Version from GitHub

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/installation

This command clones the Bedtools development repository from GitHub using Git. This allows users to access the latest bug fixes and features before they are officially released. The cloned repository can then be compiled using the source compilation instructions.

```bash
git clone https://github.com/arq5x/bedtools2.git
```

--------------------------------

### GFF File Example

Source: https://bedtools.readthedocs.io/en/latest/content/general-usage

An example entry demonstrating the required nine columns for the GFF file format, including seqname, source, feature, start, end, score, strand, frame, and attribute.

```gff
seq1	blASTX	similarity	101	235	87.1	+	0	Target "HBA_HUMAN" 11 55 ;
E_value 0.0003
dJ102G20	GD_mRNA	coding_exon	7105	7201	.	-	2	Sequence "dJ102G20.C1.1"
```

--------------------------------

### bedtools closest Usage Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/closest

This example demonstrates the basic command structure for bedtools closest, specifying input files for the query (-a) and database (-b) features. It's crucial that both input files are presorted by chromosome and start position for correct operation.

```bash
bedtools closest [OPTIONS] -a <FILE> \
                             -b <FILE1, FILE2, ..., FILEN>
```

```bash
closestBed [OPTIONS] -a <FILE> \
                       -b <FILE1, FILE2, ..., FILEN>
```

--------------------------------

### BEDTools overlap example with windowBed

Source: https://bedtools.readthedocs.io/en/latest/content/tools/overlap

This example demonstrates piping the output of 'bedtools window' into the 'overlap' command. It specifies the relevant columns for start and end coordinates from the piped input to calculate overlap or distance.

```bash
bedtools window -a A.bed -b B.bed -w 10 | overlap -i stdin -cols 2,3,6,7
chr1  10  20  A  chr1  15  25  B  5
chr1  10  20  C  chr1  25  35  D  -5
```

--------------------------------

### BEDTools Main Command Usage

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/bedtools-suite

Demonstrates the general syntax for invoking BEDTools sub-commands. Requires BEDTools to be installed and in the system's PATH.

```bash
bedtools [sub-command] [options]
```

--------------------------------

### Install zlib Development Libraries on Ubuntu

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/faq

These commands are used to install the zlib development libraries on Ubuntu systems, which are required for compiling tools like bedtools that depend on zlib functionality. Ensure you have sudo privileges to run these commands.

```bash
sudo apt-get install zlib1g-dev
sudo apt-get install zlib
```

--------------------------------

### linksBed Usage Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/links

Demonstrates the basic usage of linksBed to create an HTML file from a BED/GFF/VCF input file. The output is redirected to an HTML file for viewing in a web browser.

```bash
linksBed -i genes.bed > genes.html
```

--------------------------------

### BED file format example

Source: https://bedtools.readthedocs.io/en/latest/content/overview

Illustrates a single basepair feature in BED format. BED format uses 0-based start and 1-based end coordinates.

```plaintext
chr1   0        1    first_base
```

--------------------------------

### bed12ToBed6 Input and Output Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/bed12tobed6

Illustrates the transformation of BED12 data to BED6 format using bed12ToBed6 with piped input. The example shows how a single BED12 entry with multiple blocks (exons) is converted into several distinct BED6 entries, each representing one block.

```bash
head data/knownGene.hg18.chr21.bed | tail -n 3 | bed12ToBed6 -i stdin
chr21 10079666  10080194  uc002yiv.1 0  -
chr21 10081596  10081687  uc002yiv.1 0  -
chr21 10119416  10119517  uc002yiv.1 0  -
chr21 10120593  10120808  uc002yiv.1 0  -
chr21 10080031  10080231  uc002yiw.1 0  -
chr21 10081596  10081687  uc002yiw.1 0  -
chr21 10081660  10081687  uc002yix.2 0  -
chr21 10119416  10119517  uc002yix.2 0  -
chr21 10120573  10120796  uc002yix.2 0  -
```

--------------------------------

### bedtools multiinter -empty usage example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/multiinter

Demonstrates the command-line usage of bedtools multiinter with the -header, -names, -empty, and -g options, including sample input files and the resulting output.

```bash
$ bedtools multiinter -header -names A B C -i a.bed b.bed c.bed -empty -g sizes.txt
```

--------------------------------

### Bedtools groupby: Default Behavior Example (Bash)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/groupby

Illustrates the default behavior of bedtools groupby by showing how to prepare input data for analysis. The example uses a 'cat' command to display the contents of a hypothetical 'variants.bed' file, which would typically be pre-processed before being piped to bedtools groupby.

```bash
cat variants.bed
```

--------------------------------

### Bedmap Command Examples for Comparison

Source: https://bedtools.readthedocs.io/en/latest/_sources/index

Provides examples of using the 'bedmap' command for comparison with bedtools intersect. It shows commands both with and without the '--ec' option for error checking, illustrating different modes of operation.

```bash
# bedmap (without error checking)
$ bedmap --echo --count --bp-ovr 1 \
         ccds.exons.bed aln.bam.bed
```

```bash
# bedmap (no error checking)
$ bedmap --ec --echo --count --bp-ovr 1 \
         ccds.exons.bed aln.bam.bed
```

--------------------------------

### bedtools coverage with sorted input for memory efficiency

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/coverage

This example shows how to use the '-sorted' option when input files are presorted by chromosome and start position. This option invokes a memory-efficient algorithm suitable for processing very large files.

```bash
sort -k1,1 -k2,2n input.bed > input.sorted.bed
bedtools coverage -a input.sorted.bed -b others.bed -sorted
```

--------------------------------

### BED5 Format Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Example of a BED5 file format, which includes chromosome, start, end, name, and score for a genomic feature.

```plaintext
chr1	11873	14409	uc001aaa.3	0
```

--------------------------------

### BED3 Format Example

Source: https://bedtools.readthedocs.io/en/latest/content/general-usage

Demonstrates the minimal BED file format (BED3) which requires only chromosome, start, and end positions.

```bed
chr1			11873		14409
```

--------------------------------

### GFF File Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

An example entry from a GFF (General Feature Format) file, illustrating the structure for storing sequence annotation features. This format includes fields for sequence ID, source, type, start, end, score, strand, frame, and attributes.

```plaintext
seq1 BLASTX similarity 101 235 87.1 + 0 Target "HBA_HUMAN" 11 55 ;
E_value 0.0003 dJ102G20 GD_mRNA coding_exon 7105 7201 . - 2 Sequence
"dJ102G20.C1.1"
```

--------------------------------

### Genome File Format Example

Source: https://bedtools.readthedocs.io/en/latest/content/general-usage

An example of a tab-delimited genome file, listing chromosome names and their sizes in basepairs, used by bedtools for genomic coordinate calculations.

```genome
chrI	15072421
chrII	15279323
...
chrX	17718854
chrM	13794
```

--------------------------------

### Example Input BED File

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/links

A sample input file in BED format, containing genomic interval information. This file is used as input for the linksBed tool.

```bed
chr21 9928613  10012791  uc002yip.1 0  -
chr21 9928613  10012791  uc002yiq.1 0  -
chr21 9928613  10012791  uc002yir.1 0  -
chr21 9928613  10012791  uc010gkv.1 0  -
chr21 9928613  10061300  uc002yis.1 0  -
chr21 10042683 10120796  uc002yit.1 0  -
chr21 10042683 10120808  uc002yiu.1 0  -
chr21 10079666 10120808  uc002yiv.1 0  -
chr21 10080031 10081687  uc002yiw.1 0  -
chr21 10081660 10120796  uc002yix.2 0  -
```

--------------------------------

### Install zlib Development Libraries for Bedtools (Fedora/CentOS)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/faq

For Fedora or CentOS systems, install the 'zlib' and 'zlib1g-dev' packages using the yum package manager to address zlib-related compilation errors for Bedtools. These are essential for handling gzipped files.

```bash
yum install zlib
yum install zlib1g-dev
```

--------------------------------

### BEDTools Intersect Example

Source: https://bedtools.readthedocs.io/en/latest/content/bedtools-suite

Provides a practical example of using the 'intersect' sub-command to find overlapping intervals between two BED files. This highlights a common use case for BEDTools.

```bash
bedtools intersect -a a.bed -b b.bed

```

--------------------------------

### bedtools flank Percentage Resizing Example (Shell)

Source: https://bedtools.readthedocs.io/en/latest/content/tools/flank

Shows how to use the -pct option with bedtools flank to create flanking intervals based on a fraction of the original interval's length.

```shell
$ cat A.bed
chr1 100 200
chr1 500 700

################################################################
# note the flanking intervals from the second record in A.bed
# are 20bp whereas the flanking intervals from the first record
# are only 10bp
################################################################
$ bedtools flank -i A.bed -g my.genome -b 0.1 -pct
chr1  90      100
chr1  200     210
chr1  480     500
chr1  700     720

```

--------------------------------

### bedtools maskfasta Soft-Masking Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/maskfasta

Illustrates how to use the '-soft' option with bedtools maskfasta to perform soft-masking, converting specified intervals to lower-case bases.

```bash
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

$ cat test.bed
chr1 5 10

$ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out -soft

$ cat test.fa.out
>chr1
AAAAAaaaccCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
```

--------------------------------

### Compute Coverage with bedtools coverage

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/example-usage

Computes the coverage of aligned sequences on specified windows. It can output raw counts or percentages and can generate BEDGRAPH files for visualization.

```bash
bedtools coverage -a reads.bed -b windows10kb.bed | head

```

```bash
bedtools coverage -a reads.bed -b windows10kb.bed | cut -f 1-4 > windows10kb.cov.bedg

```

```bash
bedtools coverage -a reads.bed -b windows10kb.bed | \
     awk '{OFS="\t"; print $1,$2,$3,$6}' \
     > windows10kb.pctcov.bedg

```

--------------------------------

### Bedtools groupby: Summarize data by group (Bash Example)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/groupby

This example demonstrates how to use bedtools groupby to summarize data. It requires the input file to be sorted by the grouping columns, specified with the -g option. The -c option specifies the column to summarize, and -o specifies the operation to perform. Input can be from a file or standard input.

```bash
sort -k1,1 -k2,2 -k3,3 data.txt | bedtools groupby -g 1,2,3 -c 4 -o mean
```

--------------------------------

### bedtools bamtobed: Convert BAM to BED format

Source: https://bedtools.readthedocs.io/en/latest/content/example-usage

This basic command converts a BAM file ('reads.bam') into BED format, writing the output to 'reads.bed'.

```bash
bedtools bamtobed -i reads.bam > reads.bed

```

--------------------------------

### bed12ToBed6 Usage Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/bed12tobed6

Demonstrates the command-line usage of bed12ToBed6, specifying the input BED12 file or 'stdin' for piped data. This tool is designed to convert multi-part BED features into single-part BED features.

```bash
bed12ToBed6 [OPTIONS] -i <BED12>
```

--------------------------------

### Find Complement Intervals with bedtools complement

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/example-usage

Reports all intervals in a specified genome that are not covered by the input intervals. Requires an input interval file and a genome file.

```bash
bedtools complement -i repeatMasker.bed -g hg18.genome

```

--------------------------------

### bedtools jaccard Minimum Overlap Fraction (No Match) Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/jaccard

Demonstrates the effect of the -f option in bedtools jaccard when the minimum overlap fraction is not met. This example requires 60% overlap and shows the resulting output.

```bash
cat a.bed
chr1  10  20
chr1  30  40

cat b.bed
chr1  15   20

bedtools jaccard -a a.bed -b b.bed -f 0.6
```

--------------------------------

### Genome File Format Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

An example of a tab-delimited Genome file format used by bedtools to specify chromosome names and their sizes in basepairs. This is crucial for operations that require knowledge of genome structure.

```plaintext
chrI  15072421
chrII 15279323 
...
chrX  17718854
chrM  13794
```

--------------------------------

### bedtools multicov Single BAM Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/multicov

Shows how `bedtools multicov` can be used with a single BAM file, demonstrating the output format with one count column per interval.

```bash
$ bedtools multicov -bams aln1.bam -bed ivls-of-interest.bed
chr1 0       10000   ivl1    100
chr1 10000   20000   ivl2    123
chr1 20000   30000   ivl3    213
chr1 30000   40000   ivl4    335
```

--------------------------------

### bedtools bamtobed: Convert BAM to BEDPE format

Source: https://bedtools.readthedocs.io/en/latest/content/example-usage

This command converts BAM alignments into BEDPE format, which represents paired-end reads, saving the output to 'reads.bedpe'.

```bash
bedtools bamtobed -i reads.bam -bedpe > reads.bedpe

```

--------------------------------

### Install zlib Development Libraries for Bedtools (Debian/Ubuntu)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/faq

To resolve zlib errors during Bedtools compilation on Debian or Ubuntu systems, install the 'zlib' and 'zlib1g-dev' packages using the apt-get package manager. These libraries are required for decompressing gzipped files.

```bash
apt-get install zlib
apt-get install zlib1g-dev
```

--------------------------------

### bedtools maskfasta Default Behavior Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/maskfasta

Demonstrates the default hard-masking behavior of bedtools maskfasta, where specified intervals in the FASTA file are replaced with 'N's.

```bash
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

$ cat test.bed
chr1 5 10

$ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out
  
$ cat test.fa.out
>chr1
AAAAANNNNNCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
```

--------------------------------

### BEDPE Format Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Illustrates a standard BEDPE file entry, which defines pairwise genomic features.

```plaintext
chr1	100	200	chr5	5000	5100	bedpe_example1	30	+	-
chr9	1000	5000	chr9	3000	3800	bedpe_example2	100	+	-
```

--------------------------------

### bedtools multicov Default Behavior Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/multicov

Illustrates the default behavior of `bedtools multicov` by showing input BED file content and the corresponding output when counting overlaps from three BAM files.

```bash
$ cat ivls-of-interest.bed
chr1 0   10000   ivl1
chr1 10000   20000   ivl2
chr1 20000   30000   ivl3
chr1 30000   40000   ivl4

$ bedtools multicov -bams aln1.bam aln2.bam aln3.bam -bed ivls-of-interest.bed
chr1 0       10000   ivl1    100 2234    0
chr1 10000   20000   ivl2    123 3245    1000
chr1 20000   30000   ivl3    213 2332    2034
chr1 30000   40000   ivl4    335 7654    0
```

--------------------------------

### BED3 Format Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Example of a BED3 file format, which includes the chromosome, start, and end positions of a genomic feature.

```plaintext
chr1	11873	14409
```

--------------------------------

### BEDPE Format with Custom Fields Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Demonstrates a BEDPE file entry that includes additional user-defined fields for extra annotation.

```plaintext
chr1	10	20	chr5	50	60	a1	30	+	-	0	1
chr9	30	40	chr9	80	90	a2	100	+	-	2	1
```

--------------------------------

### bedtools multicov Usage Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/multicov

Demonstrates the basic command-line usage of `bedtools multicov` to count overlapping alignments from multiple BAM files against a BED file.

```bash
bedtools multicov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed  <BED/GFF/VCF>
```

```bash
multiBamCov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed  <BED/GFF/VCF>
```

--------------------------------

### Display Bedtools Top-Level Help Menu

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/faq

Access a high-level overview of available Bedtools sub-commands and their general usage by running the 'bedtools -h' command. This helps in navigating the various tools offered by Bedtools.

```bash
$ bedtools -h
bedtools: flexible tools for genome arithmetic and DNA sequence analysis.
usage:    bedtools <subcommand> [options] ...
```

--------------------------------

### bedtools getfasta: Default FASTA output

Source: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta

Demonstrates the default behavior of `bedtools getfasta` where sequences are extracted and output in FASTA format with headers like '<chrom>:<start>-<end>'.

```bash
cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

cat test.bed
chr1 5 10

bedtools getfasta -fi test.fa -bed test.bed
>chr1:5-10
AAACC

```

--------------------------------

### pairToPair Command Line Usage

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/pairtopair

The basic command-line usage for the pairToPair tool, specifying the input BEDPE files and options.

```bash
pairToPair [OPTIONS] -a <BEDPE> -b <BEDPE>
```

--------------------------------

### Comparing flankBed and slopBed output

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/history

This example contrasts the output of flankBed and slopBed when creating flanking regions. SlopBed includes the original feature in its output, while flankBed only outputs the flanking regions.

```bash
bin/flankBed -i a.bed -b 10 -g genomes/human.hg18.genome 
chr1	90	100
chr1	200	210
```

```bash
bin/slopBed -i a.bed -b 10 -g genomes/human.hg18.genome 
chr1	90	210
```

--------------------------------

### View BAM File Contents (Example)

Source: https://bedtools.readthedocs.io/en/latest/content/tools/bedtobam

Demonstrates how to view the contents of a generated BAM file using samtools view and pipe the output to head to see the first few alignments. This is useful for verifying the output format.

```bash
samtools view rmsk.hg18.chr21.bam | head -5
```

```bash
samtools view knownGene.bam | head -2
```

--------------------------------

### bedtools maskfasta Usage Summary

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/maskfasta

Provides the basic command-line syntax for using bedtools maskfasta, specifying input FASTA, feature file, and output FASTA.

```bash
$ bedtools maskfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
  
(or):

$ maskFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
```

--------------------------------

### bedtools jaccard Default Usage Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/jaccard

Demonstrates the default behavior of bedtools jaccard, calculating intersection, union, Jaccard statistic, and number of intersections between two BED files.

```bash
cat a.bed
chr1  10  20
chr1  30  40

cat b.bed
chr1  15   20

bedtools jaccard -a a.bed -b b.bed
```

--------------------------------

### Identify Uncovered Genome Intervals with bedtools complement

Source: https://bedtools.readthedocs.io/en/latest/content/example-usage

Reports genomic intervals not covered by specified input intervals. Requires an input BED file and a genome file to define the reference genome.

```bash
bedtools complement -i repeatMasker.bed -g hg18.genome
```

--------------------------------

### Bedtools: Valid Header Lines

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/overview

Provides examples of valid header lines that bedtools will ignore in BED and GFF files. These lines typically start with '#', 'track', or 'browser'.

```plaintext
track name=aligned_read description="Illumina aligned reads"
chr5 100000 500000 read1 50 +
chr5 2380000 2386000 read2 60 -

#This is a fascinating dataset
chr5 100000 500000 read1 50 +
chr5 2380000 2386000 read2 60 -

browser position chr22:1-20000
chr5 100000 500000 read1 50 +
chr5 2380000 2386000 read2 60 -
```

--------------------------------

### bedtools merge: Merge overlapping repetitive elements

Source: https://bedtools.readthedocs.io/en/latest/content/example-usage

This command merges overlapping features in 'repeatMasker.bed' into single, consolidated entries. The input file must be sorted by chromosome and then by start coordinate.

```bash
bedtools merge -i repeatMasker.bed

```

--------------------------------

### bedtools bamtobed: Convert BAM to BEDPE format

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/example-usage

Converts BAM alignment data into BEDPE format, which is suitable for paired-end reads. BEDPE represents the start and end of both reads in a pair.

```bash
bedtools bamtobed -i reads.bam -bedpe > reads.bedpe
```

--------------------------------

### Creating a Genome File with samtools faidx

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Demonstrates the process of creating a genome file suitable for bedtools using `samtools faidx`. This involves downloading a FASTA reference genome, indexing it with `samtools faidx`, and then using the resulting .fai file as the genome file for bedtools operations.

```bash
# download GRCh38
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa
# create an index of it
samtools faidx GRCh38_full_analysis_set_plus_decoy_hla.fa
# use the .fai index as a genome file with bedtools
bedtools complement my.grch38.bed -g GRCh38_full_analysis_set_plus_decoy_hla.fa.fai
```

--------------------------------

### Display Help for a Specific Bedtools Tool

Source: https://bedtools.readthedocs.io/en/latest/content/faq

Shows detailed help and options for a specific bedtools sub-command, such as 'bedtools merge'.

```bash
$ bedtools merge -h
Tool:    bedtools merge (aka mergeBed)
Version: v2.17.0
Summary: Merges overlapping BED/GFF/VCF entries into a single interval.
Usage:   bedtools merge [OPTIONS] -i <bed/gff/vcf>
Options:
    -s      Force strandedness. ...
```

--------------------------------

### BEDTools Valid Header Examples

Source: https://bedtools.readthedocs.io/en/latest/content/overview

Illustrates valid header lines that bedtools will ignore at the beginning of BED and GFF files. Headers starting with '#', 'track', or 'browser' are recognized and skipped, ensuring correct data parsing.

```plaintext
track name=aligned_read description="Illumina aligned reads”
chr5 100000 500000 read1 50 +
chr5 2380000 2386000 read2 60 -

#This is a fascinating dataset
chr5 100000 500000 read1 50 +
chr5 2380000 2386000 read2 60 -

browser position chr22:1-20000
chr5 100000 500000 read1 50 +
chr5 2380000 2386000 read2 60 -

```

--------------------------------

### Annotate BED file with coverage from other files (bedtools)

Source: https://bedtools.readthedocs.io/en/latest/content/tools/annotate

This example demonstrates the default behavior of `bedtools annotate`, where it calculates the fraction of each feature in the input file (`-i`) covered by features in the provided annotation files (`-files`). The output includes the original feature information followed by the calculated coverage fractions.

```bash
cat variants.bed
chr1 100  200   nasty 1  -
chr2 500  1000  ugly  2  +
chr3 1000 5000  big   3  -

cat genes.bed
chr1 150  200   geneA 1  +
chr1 175  250   geneB 2  +
chr3 0    10000 geneC 3  -

cat conserve.bed
chr1 0    10000 cons1 1  +
chr2 700  10000 cons2 2  -
chr3 4000 10000 cons3 3  +

cat known_var.bed
chr1 0    120   known1   -
chr1 150  160   known2   -
chr2 0    10000 known3   +

bedtools annotate -i variants.bed -files genes.bed conserve.bed known_var.bed
chr1  100     200     nasty   1       -       0.500000        1.000000        0.300000
chr2  500     1000    ugly    2       +       0.000000        0.600000        1.000000
chr3  1000    5000    big     3       -       1.000000        0.250000        0.000000
```

--------------------------------

### bedtools complement Usage Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/complement

Demonstrates the basic usage of 'bedtools complement' to find genomic regions not covered by input intervals. Requires an input BED/GFF/VCF file and a genome file.

```bash
bedtools complement -i <BED/GFF/VCF> -g <GENOME>
```

```bash
complementBed -i <BED/GFF/VCF> -g <GENOME>
```

```bash
$ cat A.bed
chr1  100  200
chr1  400  500
chr1  500  800

$ cat my.genome
chr1  1000
chr2  800

$ bedtools complement -i A.bed -g my.genome
chr1  0   100
chr1  200 400
chr1  800 1000
chr2  0   800
```

--------------------------------

### bedtools genomecov Usage Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov

Shows the basic usage pattern for bedtools genomecov, including options for input files (-i, -ibam) and genome file (-g). It demonstrates alternative command names like 'genomeCoverageBed'.

```bash
bedtools genomecov [OPTIONS] [-i|-ibam] -g (iff. -i and not -ibam)
```

```bash
genomeCoverageBed [OPTIONS] [-i|-ibam] -g (iff. -i and not -ibam)
```

--------------------------------

### Merge Overlapping Intervals with bedtools merge

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/example-usage

Merges overlapping repetitive elements into a single entry. The input must be sorted by chromosome and then by start coordinate. For BED files, pre-sorting is required using 'sort -k1,1 -k2,2n'.

```bash
bedtools merge -i repeatMasker.bed
```

```bash
bedtools merge -i repeatMasker.bed -n
```

```bash
bedtools merge -i repeatMasker.bed -d 1000
```

--------------------------------

### bedtools getfasta Usage Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/getfasta

This snippet shows the basic command-line usage of bedtools getfasta, specifying the input FASTA file (-fi) and the BED/GFF/VCF file (-bed). Output can be directed to stdout or a specified output file (-fo).

```bash
$ bedtools getfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF>

```

```bash
$ getFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF>

```

--------------------------------

### bedtools coverage with sorted input for large files

Source: https://bedtools.readthedocs.io/en/latest/content/tools/coverage

This example shows how to use the '-sorted' option with bedtools coverage for processing very large files. It requires the input files to be pre-sorted by chromosome and start position to enable a memory-efficient algorithm.

```bash
sort -k1,1 -k2,2n in.bed > in.sorted.bed
bedtools coverage -a input.bed -b large_coverage.bed -sorted
```

--------------------------------

### Merge Overlapping Intervals with bedtools

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/merge

This example demonstrates the default behavior of bedtools merge, combining overlapping and book-ended intervals in a BED file into a single, larger interval. The input file must be presorted by chromosome and start position.

```bash
cat A.bed
chr1  100  200
chr1  180  250
chr1  250  500
chr1  501  1000

bedtools merge -i A.bed
chr1  100  500
chr1  501  1000
```

--------------------------------

### BEDTools General Command Structure

Source: https://bedtools.readthedocs.io/en/latest/content/bedtools-suite

Demonstrates the basic command-line syntax for invoking BEDTools and its sub-commands. This is the fundamental way to interact with the suite.

```bash
bedtools [sub-command] [options]

```

--------------------------------

### BEDTools overlap: Compute overlap from windowBed output

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/overlap

This example demonstrates how to pipe the output of 'bedtools window' into the 'overlap' command to calculate the overlap between features. The '-i stdin' option is used to read from the pipe, and '-cols 2,3,6,7' specifies the columns containing the start and end coordinates from the piped input.

```bash
bedtools window -a A.bed -b B.bed -w 10 | overlap -i stdin -cols 2,3,6,7
```

--------------------------------

### GFF Format Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Provides an example of a typical GFF file entry, used for annotating genomic features.

```plaintext
# GFF entries would typically look like this, though not explicitly provided in the text.
```

--------------------------------

### bedtools getfasta: Output to file

Source: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta

Shows how to redirect the output of `bedtools getfasta` to a specified output file using the -fo option.

```bash
bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out

cat test.fa.out
>chr1:5-10
AAACC

```

--------------------------------

### BED4 Format Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Example of a BED4 file format, extending BED3 by adding a name for the genomic feature.

```plaintext
chr1	11873	14409	uc001aaa.3
```

--------------------------------

### Filter and Convert BAM to BED with samtools and bedtools

Source: https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed

This example demonstrates piping the output of samtools view to bedtools bamtobed to convert only properly-paired reads (FLAG == 0x2) into BED format. The input is specified as stdin, and the output is piped to head for preview.

```bash
$ samtools view -bf 0x2 reads.bam | bedtools bamtobed -i stdin | head
chr7   118970079   118970129   TUPAC_0001:3:1:0:1452#0/1   37   -
chr7   118965072   118965122   TUPAC_0001:3:1:0:1452#0/2   37   +
chr11  46769934    46769984    TUPAC_0001:3:1:0:1472#0/1   37   -
chr11  46765606    46765656    TUPAC_0001:3:1:0:1472#0/2   37   +
chr20  54704674    54704724    TUPAC_0001:3:1:1:1833#0/1   37   +
chr20  54708987    54709037    TUPAC_0001:3:1:1:1833#0/2   37   -
chrX   9380413     9380463     TUPAC_0001:3:1:1:285#0/1    0    -
chrX   9375861     9375911     TUPAC_0001:3:1:1:285#0/2    0    +
chrX   131756978   131757028   TUPAC_0001:3:1:2:523#0/1    37   +
chrX   131761790   131761840   TUPAC_0001:3:1:2:523#0/2    37   -    
```

--------------------------------

### BED6 Format Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Example of a BED6 file format, adding strand information to the BED5 format for genomic features.

```plaintext
chr1	11873	14409	uc001aaa.3	0	+
```

--------------------------------

### Check Bedtools Version

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/faq

To determine the installed version of Bedtools, use the '--version' command-line option. This is useful for verifying installation and compatibility.

```bash
$ bedtools --version
bedtools v2.17.0
```

--------------------------------

### bedtools bamtobed Usage Summary

Source: https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed

This shows the basic command structure for bedtools bamtobed, indicating the required input file and the alternative command name 'bamToBed'.

```bash
bedtools bamtobed [OPTIONS] -i <BAM>

bamToBed [OPTIONS] -i <BAM>
```

--------------------------------

### BED12 Format Example

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/general-usage

Example of a BED12 file format, representing a genomic feature with all twelve possible columns, including block information.

```plaintext
chr1	11873	14409	uc001aaa.3	0	+	11873	11873	0	3	354,109,1189,	0,739,1347,
```

--------------------------------

### bedtools jaccard Usage Summary

Source: https://bedtools.readthedocs.io/en/latest/content/tools/jaccard

Provides the basic usage syntax for the bedtools jaccard command, including required input files and available options.

```bash
bedtools jaccard [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
```

--------------------------------

### bedtools intersect: BAM to BED conversion with overlap filtering

Source: https://bedtools.readthedocs.io/en/latest/content/example-usage

This example converts BAM alignments to BED format and filters them to retain only those overlapping 'exons.bed', outputting the result to 'reads.touchingExons.bam'.

```bash
bedtools intersect -abam reads.bam -b exons.bed > reads.touchingExons.bam

```

--------------------------------

### flank: Prevent Flanks Before Chromosome Start

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/history

Ensures that 'bedtools flank' no longer attempts to calculate flanks prior to the start of a chromosome. This corrects off-by-one errors and invalid coordinate issues.

```shell
# Example: Calculating flanks, respecting chromosome boundaries
bedtools flank -i intervals.bed -g chromsizes.txt -l 100 -r 100
```

--------------------------------

### bedtools window - BAM Input (-abam) and BED Output (-bed)

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/window

Demonstrates using a BAM file as input for file A with the -abam option and specifying BED format for the output with the -bed option. This is useful for processing alignment data.

```bash
bedtools window -abam reads.bam -b genes.bed -bed
```

--------------------------------

### linksBed with Custom UCSC Mirror, Organism, and Build

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/links

Illustrates advanced usage of linksBed, allowing customization of the UCSC Genome Browser mirror, organism, and genome build. This provides granular control over the generated links.

```bash
linksBed -i genes.bed -base http://mirror.uni.edu -org mouse -db mm9 > genes.html
```

--------------------------------

### bedtools flank: Prevent Flanking Before Chromosome Start

Source: https://bedtools.readthedocs.io/en/latest/content/history

The 'bedtools flank' tool has been fixed to no longer attempt to take flanks prior to the start of a chromosome. This prevents erroneous output and ensures biologically meaningful results.

```bash
# Example usage of bedtools flank
bedtools flank -i intervals.bed -g genome.txt -l 100 -r 100
```

--------------------------------

### bedtools multiinter with Header Option

Source: https://bedtools.readthedocs.io/en/latest/_sources/content/tools/multiinter

Example of using the -header option with bedtools multiinter to include column names in the output. This enhances readability by labeling the 'num' and 'list' columns, as well as the input files.

```bash
bedtools multiinter -header -i a.bed b.bed c.bed
chrom	start	end	num	list	a.bed	b.bed	c.bed
chr1	6	8	1	1	1	0	0
chr1	8	12	2	1,3	1	0	1
chr1	12	15	3	1,2,3	1	1	1
chr1	15	20	2	1,2	1	1	0
chr1	20	22	1	2	0	1	0
chr1	22	30	2	1,2	1	1	0
chr1	30	32	1	2	0	1	0
chr1	32	34	1	3	0	0	1
```

--------------------------------

### Bedtools Subtract Basic Usage Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/subtract

Demonstrates the default behavior of bedtools subtract where overlapping portions of intervals in B are removed from A. If B completely overlaps A, the A feature is removed. This example shows a case where a portion of A remains.

```bash
cat A.bed
chr1  10   20
chr1  100  200

cat B.bed
chr1  0    30
chr1  180  300

bedtools subtract -a A.bed -b B.bed
chr1  100  180
```

--------------------------------

### Compute BAM Alignment Coverage on Exons with Bedtools

Source: https://bedtools.readthedocs.io/en/latest/content/advanced-usage

This example demonstrates computing coverage of BAM alignments on exons using bedtools bamtobed and coverage. It converts BAM reads to BED format and then calculates coverage against exon intervals. Dependencies include samtools and bedtools.

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

--------------------------------

### bedtools jaccard Minimum Overlap Fraction Example

Source: https://bedtools.readthedocs.io/en/latest/content/tools/jaccard

Illustrates how to use the -f option in bedtools jaccard to require a minimum overlap fraction with respect to intervals in file A. This example shows the output when requiring 10% overlap.

```bash
cat a.bed
chr1  10  20
chr1  30  40

cat b.bed
chr1  15   20

bedtools jaccard -a a.bed -b b.bed -f 0.1
```

--------------------------------

### View Header of Genome File with bedtools

Source: https://bedtools.readthedocs.io/en/latest/content/tools/summary

This snippet displays the first few lines of the prepared genome file using the `head` command. This helps in confirming the correct format and content for use with `bedtools summary`.

```shell
head grch38.genome.txt
```