Difference between revisions of "Bam2tdf"

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(Created page with "BAM2TDF is a command-line tool that converts BAM files to TDF (coverage) files. You can download the latest version from the GenomeView nightly builds: http://genomeview.org/...")
 
 
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You can download the latest version from the GenomeView nightly builds:
 
You can download the latest version from the GenomeView nightly builds:
 +
 
http://genomeview.org/jenkins/bam2tdf-nightly/
 
http://genomeview.org/jenkins/bam2tdf-nightly/
  
  ~$ java -jar bam2tdf.jar <location of your bam file>
+
Instructions:
 +
 
 +
  ~$ java -jar bam2tdf.jar [-m <minimumMappingQuality>] <location of your bam file>
 +
 
 +
 
 +
bam2tdf calculates fragment coverage, not physical coverage
  
 
Requirements:
 
Requirements:
- Java 7+
+
- Java 7+
- BAM file needs to be sorted and indexed
+
- BAM file needs to be sorted and indexed

Latest revision as of 22:25, 25 November 2013

BAM2TDF is a command-line tool that converts BAM files to TDF (coverage) files.

You can download the latest version from the GenomeView nightly builds:

http://genomeview.org/jenkins/bam2tdf-nightly/

Instructions:

~$ java -jar bam2tdf.jar [-m <minimumMappingQuality>] <location of your bam file>


bam2tdf calculates fragment coverage, not physical coverage

Requirements:

- Java 7+
- BAM file needs to be sorted and indexed