Bam2SVG

##Motivation

display a BAM as SVG

##Compilation

See also Compilation.

$ make bam2svg

##Synopsis

$ java -jar dist/bam2svg.jar [options] (stdin|file.bam) 

##Options

Option	Description
-h	get help (this screen) and exit.
-v	print version and exit.
-R (file)	The reference sequence as a FASTA file and indexed with samtools faidx.
-S (file)	add VCF indexed with tabix. Optinal. the Samples's name must be the same than in the BAM.
-i position	(chrom:start-end) interval. Required.
-w (width)	Page width
-L (level)	log level. One of java.util.logging.Level . Optional.
--doap	prints a DOAP+XML description of the program and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/bam2svg/BamToSVG.java

##Example

$ java -jar dist/bam2svg.jar \
    -R human_g1k_v37.fasta \
    -i "19:252-260" \
    -S variants.vcf.gz \
    file.bam > out.svg

Gallery

https://twitter.com/yokofakun/status/523031098541232128

https://twitter.com/yokofakun/status/522415314425090048

##See also

##History

• 2014: Creation