Question: Why ExAC used bwa aln instead of mem?
3
gravatar for abascalfederico
2.4 years ago by
abascalfederico1.1k
Spain
abascalfederico1.1k wrote:

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 ...
bwa exac • 880 views
ADD COMMENTlink written 2.4 years ago by abascalfederico1.1k
1

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by RamRS24k

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.

ADD REPLYlink written 2.4 years ago by abascalfederico1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1107 users visited in the last hour