what is the insertPenalty for -U option of bwa mem?
0
0
Entering edit mode
20 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!

bwa-mem • 362 views
ADD COMMENT

Login before adding your answer.

Traffic: 1696 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6