Question: BWA option about the insert size
gravatar for xieduo9394
3.5 years ago by
xieduo93940 wrote:


I am using BWA to do alignment and estimate the insert size of my data and the excepted insert size length is 2000bp,so I use the "sampe" command to do alignment,but I found "-a" option is available,and the description of this option is:

Maximum insert size for a read pair to be considered being mapped properly. Since 0.4.5, this option is only used when there are not enough good alignment to infer the distribution of insert sizes. [500]

I use this option and set it to "-a 2000", but I don't know clearly what impact will this option have on my result?Should I use this option?


bwa pair-end alignment genome • 2.1k views
ADD COMMENTlink written 3.5 years ago by xieduo93940

If this is standard illumina sequencing it is unlikely that your inserts are 2kb in size. If you have a reference available you can easily figure out the insert size using from BBMap suite. ref=ref.fasta in1=r1.fq in2=r2.fq ihist=ihist.txt

ADD REPLYlink written 3.5 years ago by genomax92k

Without reference, and much faster, is BBMerge (what a surprise that it's part of BBMap!), with a little command line addition to catch output in a text file and allow it to be output to screen also: in1=r1.fq in2=r2.fq out=merged.fq 2>&1 | tee insert.txt
ADD REPLYlink written 3.4 years ago by bruce.moran860

This will only work when there are reads (I am not sure how many need to) that overlap.

ADD REPLYlink written 3.4 years ago by genomax92k
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