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 21:25, 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