pslCDnaFilter -filterWeirdOverlapped  -bestOverlap /gbdb/sacBay2/Sbay.psl /gbdb/sacBay2/cdnafilt.psl 
pslCDnaFilter -filterWeirdOverlapped  -bestOverlap /gbdb/sacMik2/Smik.psl /gbdb/sacMik2/cdnafilt.psl 

pslToBed /gbdb/sacBay2/cdnafilt.psl /gbdb/sacBay2/cdnafilt.bed
pslToBed /gbdb/sacMik2/cdnafilt.psl /gbdb/sacMik2/cdnafilt.bed

hgLoadBed sacBay2 baseannotation /gbdb/sacBay2/cdnafilt.bed
hgLoadBed sacMik2 baseannotation /gbdb/sacMik2/cdnafilt.bed