Bwa Alignment: Gap Vs Soft-Clipped Sequences
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12.1 years ago
michealsmith ▴ 790

Suppose we have a 30bp-50bp deletion, and read length is 100bp. If the read happens to cover the deletion, I'm just wondering, will BWA align the read with soft-clipped sequences, or allow this 30bp-50bp gap?

I'm pretty much sure for deletion like 10bp or even up to 20bp, BWA can do the gapped alignment; and for deletions, say 70, 80bp, BWA will produce split reads. But I'm just confused about this middle state.

Thanks a lot!

bwa • 4.9k views
Entering edit mode
12.1 years ago

This is very dependent on the options you use on your 'bwa aln' incantation. Although I don't believe 'bwa' was designed to map reads with such large indels. From my experience, I use it for mappings with a handful of indels, not much more.

This being said, you can tweak some options to allow for more indels. You can for instance have a look at these two options on 'bwa aln':

  • -o INT maximum number or fraction of gap opens
  • -e INT maximum number of gap extensions

Otherwise, you can also use novoalign, stampy or blat which may handle large indels better than bwa.

Entering edit mode

thanks. But can you explain "fraction of gap opens" and "gap extensions" more?


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