Hello.

What does "Penalties for 5'-end and 3'-end clipping" mean in BWA-MEM? Does it refer to both soft and hard clipping?

How can I prevent soft/hard clipping?

I assumed that the more figure for clipping penalty means the less clipping. But when the "Penalties for 5'-end and 3'-end clipping=0,0", only 117 bases were soft clipped in one of the reads in my NGS data, and when I increased it to 5,5 , 145 bases were clipped.

Thanks in advance.