Bedtools Bam to Bed

Bedtools is a powerful suite of command line tools for dealing with genomic data. One of its most commonly used tools is bamToBed, which converts BAM files into the BED format.

Installation

Bedtools can be installed using the following command:

$ conda install -c bioconda bedtools

Usage

The basic usage of bamToBed is:

$ bedtools bamToBed -i input.bam > output.bed

This will take the BAM file input.bam and convert it into the BED file output.bed.

By default, bamToBed will output the coordinates of each read in the BED format. For paired-end reads, it will output both the coordinates of the first read and the coordinates of the second read in separate rows.

Advanced Usage

There are several options that can be used with bamToBed to modify its behavior:

• -bed12: output 12-column BED format, including block sizes and gaps for spliced alignments
• -split: split reads with Ns in CIGAR into individual exons
• -mate1, -mate2: output only the first or second mate of paired-end reads
• -iout, -iout_offset: modify output coordinates by a fixed amount

Examples

Paired-End Reads

To convert only the second mate of paired-end reads, use the -mate2 option:

$ bedtools bamToBed -mate2 -i input.bam > output.bed

Spliced Alignments

To output the coordinates of each exon instead of the entire read, use the -split option:

$ bedtools bamToBed -split -i input.bam > output.bed

Modified Coordinates

To adjust the output coordinates by a fixed amount, use the -iout and/or -iout_offset options:

$ bedtools bamToBed -iout BEDPE -iout_offset 250 -i input.bam > output.bed

This will convert the BAM file into a BEDPE file (which includes both mates of a paired-end read in a single row), and will offset the coordinates by 250 base pairs.

Conclusion

bamToBed is a useful tool for converting BAM files into the BED format. With its many options and advanced features, it can be customized to fit a wide variety of use cases.