lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
GNU General Public License v3.0
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-Y -M should use or not? #274

Open tamadezhenshiyuncai opened 4 years ago

tamadezhenshiyuncai commented 4 years ago

-Y use soft clipping for supplementary alignments -M mark shorter split hits as secondary

i don't know when to add these two parameters, and when not to add, could you give some advice, appreciate