what is the insertPenalty for -U option of bwa mem?
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19 months ago
yifangt86 ▴ 60

Hello, I was trying to look at the scores of paired and unpaired alignments of my paired-end reads(FASTQ) on a reference with bwa mem. From the manual the -U option says:

-U INT  Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as scoreRead1+scoreRead2-INT and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these two scores to determine whether we should force pairing. [9]

From the help information:

   $ bwa mem
    -U INT        penalty for an unpaired read pair [17]

I believe the default INT values 9 and 17 is from different version of bwa, but I have a confusion between the INT value and the insertPenalty for the score calculations for paired and unpaired reads. I could guess the meaning of insertPenalty literally, but the manual seems not have a detailed explanation or the option to set it.

My question is: What is exactly the insertPenalty for this -U option setting and how to customize it instead of the default value(if any)?

Thanks a lot!

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