Overview

In bioinformatics, a common task is to align several (usually short) DNA sequences against a reference sequence (e. g. a complete genome of the organism).

The screenshot of shows the alignment of several short DNA sequences (reads) against a reference genome. The program graphically displays the coverage track

IGV itself displays a coverage track, but for computational reasons only if the zoom is below 50 kbp. On the other hand, it is possible to visualize a BED track spanning the whole chromosome.

bamtocov reads an alignment file in BAM format and prints a BED track with the nucleotide coverage and can be used to select the regions with a coverage of interest (e. g. uncovered regions with 0X coverage, low coverage regions <5X, etc.).

Features

can read sorted BAM files even without the index

can read sorted BAM files from streams (from a pipe)

can calculate the physical coverage to check the assembly integrity

can calculate the per-strand coverage to check for strand bias

lowest memory usage for a coverage tool

File formats

BED files

A BED file (.bed) is a tab-delimited text file that defines a feature track. In this context the magnitude refers to the nucleotide coverage of the interval.

The columns are chromosome name, start position (inclusive, zero-based), end position (non-inclusive, zero-based) and coverage. An example is:

seq1    0       9       0
seq1    9       109     5
seq1    109     189     0
seq1    189     200     2

Target statistics

this format is not final.

For each sample, 5 columns are printed:

• bam_bases
• bam_mean
• bam_min
• bam_max
• bam_length

Further reading

For a more detailed introduction to coverage analysis see: Coverage Analysis from the Command Line.