mozack
can vdjer work on whole-exome sequencing data?
Hello,
can vdjer work on whole-exome sequencing data? or how to adjust the parameters to make it work for whole-exome sequencing data?
Thanks much!
Hi,
We've not tested on exome data. I would be skeptical about using exome data as the exome targets may not actually capture BCR sequences.
Good morning and thank you so much for your prompt reply. We looked at our exome targets and quite sure that all the BCR gene segments were covered, that’s why we’d like to give it a try. In this case, what parameters do you suggest to change?
Thanks much!
From: Lisle Mose [email protected] Reply-To: mozack/vdjer [email protected] Date: Friday, August 11, 2017 at 7:59 AM To: mozack/vdjer [email protected] Subject: Re: [mozack/vdjer] can vdjer work on whole-exome sequencing data? (#9)
Hi,
We've not tested on exome data. I would be skeptical about using exome data as the exome targets may not actually capture BCR sequences.
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OK. Keep in mind that somatic hypermutation may have some impact on the capture.
I would suggest trying with the standard params and then try the sensitive mode if that yields no results.
Many Thanks! what's the default distance between V and J anchors? Do you suggest to change that?
For IGH we allow 10-90 nt between anchors and for IGK/IGL 0-60nt. I would expect those defaults to still be reasonable.