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 ...