https://github.com/sandyjmacdonald/bam_coverage

Calculates coverage stats for a .bam mapping file.
https://github.com/sandyjmacdonald/bam_coverage

Last synced: about 2 months ago
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Calculates coverage stats for a .bam mapping file.

• Host: GitHub
• URL: https://github.com/sandyjmacdonald/bam_coverage
• Owner: sandyjmacdonald
• License: mit
• Created: 2014-09-21T15:53:58.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-09-21T16:27:23.000Z (over 10 years ago)
• Last Synced: 2024-04-21T04:04:58.366Z (9 months ago)
• Language: Shell
• Size: 125 KB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
bam_coverage.sh

============

Given a .bam file, the scripts calculates the miniumum, 

maximum, mean, median and standard deviation coverage.

### Dependencies

Requires [Samtools](http://www.htslib.org) to parse the .bam file and

return the depths across the mapping file.

### Usage

    ./bam_coverage.sh 

### Tips

You'll need to make the script executable with either:

    chmod a+x bam_coverage.sh

or alternatively:

    chmod 777 bam_coverage.sh

If you want to run the script on several .bam files in a directory and 

capture the information returned in a text file then try this:

    ls *.bam | xargs -I bamfile ./bam_coverage.sh bamfile