Why ExAC used bwa aln instead of mem?
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 ...
• 2,468 views
•
link
written
by
abascalfederico
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Alignment tool for very short reads (25bp)
written by Anisur Rahman •
-
Meaningful Names in BWA Alignment For Salmon?
written by pearl2070 •
-
repeating bwa alignment
written by gubrins
-
bwa output : [bwa_aln_core] calculate SA coordinate... Killed
written by deepak.sharma •
-
BWA-mem alignment is not giving desired output
written by micro32uvas •
-
bwa mem failed to allocate memory
written by cmo
-
BWA or SMALT mapping algorithm
written by P.NJ •
-
BWA MEM and ancient DNA
written by smilefreak
-
bwa mem mismatch option
written by Varun Gupta
-
Cigar And Sequence Length Are Inconsistent In Sam File
written by xiaoyanli82 •
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
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.