Wig format

The Wiggle format is used to plot quantitaitve data in a genome browser, and a detailed description can be found at this website (genome.ucsc.edu).

The native output of "BamToCov" is BED, and specifically bedGraph, that can be converted to bigWig via bedGraphToBigWig.

For convenience we report some succint examples taken from the website aforementioned.


Variable step

This format is used for data with irregular intervals between new data points, and is the more commonly used wiggle format. The span parameter is optional.

variableStep chrom=chr21 span=5
9411191	50
9411196	40
9411201	60
9411206	20
9411211	20
track type=wiggle_0 name="variableStep" description="variableStep format" visibility=full autoScale=off viewLimits=0.0:25.0 color=50,150,255 yLineMark=11.76 yLineOnOff=on priority=10
variableStep chrom=chr19 span=150
49304701 10.0
49304901 12.5
49305401 15.0
49305601 17.5
49305901 20.0
49306081 17.5
49306301 15.0
49306691 12.5

The variableStep format becomes very inefficient when there are only a few data points per 1,024 bases.

Fixed step

fixedStep chrom=chr3 start=400601 step=100 span=5

start, step and span are all optional.