Why ExAC used bwa aln instead of mem?
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4.3 years ago
abascalfederico ★ 1.2k

Anyone knows why in ExAC they used bwa aln instead of mem? I am not sure of the read lengths but somewhere said something about 150 bps x 2. Does it make sense to use bwa aln here? I though for long reads mem was the best choice

The actual parameters used in ExAC were:

bwa aln q 5 -l 32 -k 2  -o 1 ...
bwa sampe -T -P ...

exac bwa • 1.3k views
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If you can cite your source for this, that'd be great. I'm sure Daniel MacArthur's team would be glad to answer your question by the way - you could just send them an email!

EDIT: Found the source: https://www.nature.com/article-assets/npg/nature/journal/v536/n7616/extref/nature19057-s1.pdf (supplementary in the paper

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I'll send them an email, thanks for the suggestion. Regarding the use of bwa aln, I found it in the supplementary material of: Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., ... & Tukiainen, T. (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285-291.