<![CDATA[BOL: BamView: a free interactive display of read alignments in BAM data files]]> https://bioinformaticsonline.com/bookmarks/view/38172/bamview-a-free-interactive-display-of-read-alignments-in-bam-data-files? https://bioinformaticsonline.com/bookmarks/view/38172/bamview-a-free-interactive-display-of-read-alignments-in-bam-data-files Fri, 09 Nov 2018 13:43:22 -0600 https://bioinformaticsonline.com/bookmarks/view/38172/bamview-a-free-interactive-display-of-read-alignments-in-bam-data-files <![CDATA[BamView: a free interactive display of read alignments in BAM data files]]> To run the application on UNIX from the downloaded jar file run the UNIX:

java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

 

Address of the bookmark: http://bamview.sourceforge.net/

]]> Neel