The University Wiki Service was upgraded to Confluence 7.13.7. Please refer to the University Wiki Service Help Pages for a list of changes.
If you encounter any issues with the new version, submit a ticket by emailing us at help@wikis.utexas.edu.
Page tree

Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.


Introduction to Samtools - manipulating and filtering bam files

As Nathan we showed you yesterday, the main type of output from aligning reads to a databases is a binary alignment file, or BAM file. These files are compressed, so they can't be viewed using standard unix file viewers such as more, less and head. Samtools allows you to manipulate the .bam files - they can be converted into a non-binary format (SAM format specification here) and can also be ordered and sorted based on the quality of the alignment. This is a good way to remove low quality reads, or make a BAM file restricted to a single chromosome.