Bwa What Is In .Sai File

Question

[Sara]

Hello,

I would like to know what is in .sai file after alignment with BWA. what should be remove before convert it to bam file

please advise thanks Sarm

Answer 1

[Damian Kao]

Why do you want to remove anything from the .sai file? Why not convert it to .sam and then do your filtering?

.sai files are not a standardized file format and how bwa interprets/generates the files changes between versions of bwa.

I would convert it to .sam and not use the .sai files.

Answer 2

[Fidel]

The .sai file is an intermediate file containing the suffix array indexes. Such file is afterwards translated into a SAM file.

The BWA paper may help you to understand how the mapping is done:

http://bioinformatics.oxfordjournals.org/content/25/14/1754.full