Tracks

Genomic Tracks

The Bamformatics toolkit can summarize alignment files by means of genomic tracks.

Coverage

Coverage tracks are a standard means to indicate the number of reads aligned on genomic regions. The tracks can be produced via the command

java -jar Bamformatics.jar tracks –-type coverage
--bam alignment.bam --output covdir 
options

The output will be a new directory with one file per chromosome. Each track is a table in run-length encoded format. The first column shows the length (in base paits) of segment of constant coverage, the second column gives the coverage value on that segment.

The last field in the command, options, refers to details/thresholds used during variant calling. These options can also be used here to obtain the exact coverage values used during variant calling (ignoring low mapping quality, low base qualities, bases from read starts and ends, and overlapping paired-end reads).

Note: Default values for variant calling options are automatically used in calculation of coverage tracks.

Comment: The coverage tracks output by this program are in a format that can be processed by genomic track smoothing software, e.g. Locsmoc.

Other tracks

The toolkit can also compute other types of tracks: entropy of reference/alternative base pairs in an alignment, and read start and read end locations. These tracks can be produced by changing the –-type option. See the command-line help menus for more information.