BamGenScan

##Motivation

Plot the coverage of one or more BAMs. Save a picture as JPG.

Duplicates are removed.

##Compilation

See also Compilation.

$  ant bamgenscan

##Synopsis

$ java -jar dist/bamgenscan.jar [options] -o fileout.jpg \
           sample1a.bam:sample1b.bam:sample1c.bam \
           sample2a.bam \
           sample3a.bam:sample3b.bam

##Options

Please use option '-h' to get a complete list of the available options.

Option	Description
-o (file.jpg)	file out
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/genscan/BamGenScan.java

##Example

$  java -jar dist/bamgenscan.jar  --max-y 20 --image-size 2000x800  -o out.jpg f1.bam f2.bam f3.bam

the figure displays the mean, min, max, median of the coverage.

##See also

• GenScan

##History

• 2014