Bedtools
Introduction
General bioinformatics tool bult by the active Aaron Quinlan at University of Utah.
The focus of bedtools is genomic features, which can be variously defined.
Usage
bedtools is made out of various subcommands, and these may be dealt with separately
genomecov
The example in the documentation (bedtools genomecov docs) isn't very well explained, let's go over it. Note that the input is not a bam file as is more common, but a bed file, in this case.
$ cat A.bed chr1 10 20 chr1 20 30 chr2 0 500 $ cat my.genome chr1 1000 chr2 500 $ bedtools genomecov -i A.bed -g my.genome chr1 0 980 1000 0.98 chr1 1 20 1000 0.02 chr2 1 500 500 1 genome 0 980 1500 0.653333 genome 1 520 1500 0.346667
Bed files at a minimum give start and end positions on chromosomes or contigs. Here we are dealing with the minimum. The A.bed file merely states that a feature, here an arbitrary one, exists for positions 10 to 19 of chromosome 1, and 20 to 29. It's possible that they are different features because otherwise
chr1 10 30
would have also sufficed. chr2 is self-explanatory. The my.genome merely gives the total length of both chromosomes. From this, genomecov can get to work, though it focuses on giving aggregate values, not positional values, for each chromosome. So the resulting output says that therw is zero coverage of a feature in 98% of chromsome 1, and then lumps the separately lined features on chromosome 1 together, so that they represent 2% of chromosome 1. The 5th column pretty much says the same as the 3th and 4th columns.
well-known "one-liner"
Due to being a very common task, his combination of genomecov piped to awk is very popular (ref. twitter link)
bedtools genomescov -ibam aln.bam -bga | awk '$4==0' | bedtools intersect -a someregions.bed -b - > out.txt
Explanation:
- Background: A file called someregions.bed holds the chromosome ranges where features are present, but the bam file many not necessarily have the alignment
- the "$4==0" is short form awk, which means "only print if Column 4 is zero"
