Thanks for your help. Indeed from your advise, and my experience I finally find out it is better not use it, at least for variant calling. It is not recommanded or even mentioned by any variant calling pipelines, and as I mentioned above it causes unacceptable reads lost.
BWA MEM -P option
Hello everyone
I am trying to align my sequencing reads (short reads, paired-end) to reference using BWA MEM. I am wondering what is -P option really means? In BWA official manual it says -P perform SW to do mate rescue and disable reads pairing, but I didn't really get it and there is very limit interpretations about it on the internet. Here are my questions:
- What
-Pleads to compare with command without-Pin alignment? - In what condition we use
-P? - My purpose is to detect the SV and SNV, is it OK, or better/better not or makes no difference for adding
-P?
Could anyone give me some hints. Appreciate any help.
1 answer
It's actually simple. Read the instructions of the variant callers you use downstream and see whether they recommend that option or not. I personally have never seen it, nor seen it in any variant caller manual, so it's probably a "no, don't use it". It is eventually all about what the variant caller expects...or not.
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Here I ask the question by myself.
From the perspective of reads left after QC and duplication removal, there is HUGE difference of using "bwa mem -P" or not using -P.
So we can see there is about 20% reads LOST if using -P for short-reads alignment! I don't what is the proper situation for using -P, at least for short-reads alignment and variant calling pipeline, DO NOT use -P.