Question: Insert size distribution for BWA
0
gravatar for seta
17 months ago by
seta1.4k
Sweden
seta1.4k wrote:

Hi all,

I know that BWA mem calculates insert size distribution during mapping. However, for some problems, I think it may wrong in this calculation, so I calculated this parameter by Picard (CollectInsertSizeMetrics), but I don't sure how I can feed them into BWA mem via I option. Could you please kindly help me out on this issue?

Thanks

ADD COMMENTlink modified 17 months ago • written 17 months ago by seta1.4k

Picard is only reading what bwa calculated, so I doubt you gain anything.

ADD REPLYlink written 17 months ago by ATpoint42k

OK, thanks for your point. What do you think about wrong insert size estimation by bwa mem, is it possible? If I should use the alternative calculator for getting insert size distribution, then feed to bwa mem?

ADD REPLYlink written 17 months ago by seta1.4k

Usually you could estimate the library fragment size distribution from a gel or bioanalyzer results before sequencing, then compare to the fragment size estimated by BWA. Or you may map using another read aligner and compare that estimation with BWA.

ADD REPLYlink written 17 months ago by Vitis2.4k

Is this any non-standard library? What kind of experiment is it? Is this maybe something transformed back to fastq from bam without shuffling reads?

ADD REPLYlink modified 17 months ago • written 17 months ago by ATpoint42k

It's whole genome sequencing by Illumina (100bp PE). I posted the original problem here, could you please take a look at it or I explain again here?

ADD REPLYlink modified 17 months ago • written 17 months ago by seta1.4k

Yeah this is pretty much what I was suspecting. You will have quite some multimapping because of the HLA allelel so it is not unexpected that insert size calculation is off. That is why bwa expects random read order so that normally most reads in the batch of reads that is processed together come from well-mappable regions and stabilize insert size estimation. I have no experience towards HLA mapping, so I cannot contribute any further but will ask around in the Slack if someone has a recommendation.

ADD REPLYlink written 17 months ago by ATpoint42k

Thanks for your feedback. Assuming the insert size estimation by bwa mem may be wrong, could you please tell me how I can define the insert size distributions (which I calculated by picard) for bwa mem via I option?

ADD REPLYlink written 17 months ago by seta1.4k
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