BAM Index process

Question

[t.marvin.christian]

Hi there,

Just wondering, is there somebody can explain how the BAM Index made? I tried to read the samtools code so I can understand how samtools create the index for the BAM file but still don't understand. How actually the creation process of the *.bai file from BAM file?

Cheers!

Answer 1

[h.mon]

The SAM/BAM format specification describes the BAM format in detail. About the index. it has sections titled "5.1 Algorithm", "5.1.1 Basic binning index", "5.2 The BAI index format for BAM files" and "5.3 C source code for computing bin number and overlapping bins".

Probably it easier to read and understand than SAMtools code.

[t.marvin.christian]

Hi, yeah I read that part. But what about the chunk in each bin? I mean how they are formed? Or based on what the chunk is formed? For example I tried to look on the index file I found 1 bin has 8 chunks but some of them are overlap each other. Just wondering how they were formed