Bwa What Is In .Sai File
2
1
Entering edit mode
9.8 years ago
Sara ▴ 20

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

bwa • 13k views
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6
Entering edit mode
9.8 years ago

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.

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5
Entering edit mode
9.8 years ago
Fidel ★ 2.0k

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

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