Understanding SAM/BAM file specifications

The sequencing Alignment Mapping (SAM) file was designed to store the mapping data of a sample against a reference genome in a way that allow for easy downstream analysis.

In this video, I hope to go through the basic SAM file specifications based on the original documentation from Samtools. SAM file mostly consists of two sections, a header section that records information on the reference genome and experiential details, and an alignment section that records the individual nucleotide sequence difference between the samples and the reference.

Link to SAM specifications
https://samtools.github.io/hts-specs/...

Link to Slides
https://docs.google.com/presentation/...

Link to sample SAM file
https://drive.google.com/file/d/1zmyH...
https://drive.google.com/file/d/1SCu-...

How to read Cigar String
   • How to read Cigar Strings in SAM file  

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