maq map aln.map ref.bfa 1.bfq 2.bfq -a 500
-a INT max distance between two paired reads [250]
when I use -a 500 the alignmnet output also contains the pairs whose distance is larger than 500.
maq pileup
-p discard abnormal pairs
what's the standard MAQ consinder which pairs are abnormal pairs?
-a INT max distance between two paired reads [250]
when I use -a 500 the alignmnet output also contains the pairs whose distance is larger than 500.
maq pileup
-p discard abnormal pairs
what's the standard MAQ consinder which pairs are abnormal pairs?